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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 1,531 records · Page 85
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

A comprehensive study of the radiative properties of NO—a first step toward a complete air opacity

Here, in this paper we propose a methodology to calculate the radiative properties of the diatomic molecular constituents of air, and utilize the present approach to model the radiative properties of nitrogen monoxide, NO. We also investigate the important physics involved in calculating accurate radiative quantities for air, such as the Planck and Rosseland mean opacities, and emission and absorption coefficients, as well as the couplings accounted for in rovibrational calculations. Complete active space self-consistent field multi-reference configuration interaction (CAS-MRCI) calculations were performed in order to model the NO X 2 Π, a 4 Π, b 4 Σ - , 1 2 Σ + , 2 2 Σ + , 3 2 Σ + , G 2 Σ - , B' 2 Δ, (C, B) 2 2 Π, (H', L) 3 2 Π, and 1 2 Φ adiabatic states, and calculate the respective molecular data. The γ X 2 Π - A 2 Σ + , ε X 2 Π - D 2 Σ + , β' X 2 Π - B' 2 Δ, '11 000 Å' A 2 Σ + - D 2 Σ + , 'infrared' X 2 Π - X 2 Π and X 2 Π - (C, B) 2 2 Π (δ and β) band systems are investigated in monochromatic spectra calculations, as well as the Ogawa a 4 Π - b 4 Σ - band and several other band systems. Several conclusions are drawn, such as the importance of including the Ogawa band, which has not been included in previous air radiative models or comprehensive line-list calculations, as well as the importance of performing coupled rovibrational line-list calculations in order to accurately calculate the Rosseland means. We also found that the additional band systems modeled here contribute significantly to the total Planck and Rosseland means.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2017

Comparison and Assessment of Three Advanced Land Surface Models in Simulating Terrestrial Water Storage Components over the United States

In preparation for next generation North American Land Data Assimilation System (NLDAS), 3 three advanced land surface models (CLM4.0, Noah-MP, and CLSM-F2.5) were run from 1979 4 to 2014 within the NLDAS-based framework. Monthly total water storage anomaly (TWSA) and 5 its individual water storage components were evaluated against satellite-based and in situ 6 observations, and reference reanalysis products at basin-wide and statewide scales. In general, all 7 three models are able to reasonably capture the monthly and interannual variability and 8 magnitudes for TWSA. However, contributions of the anomalies of individual water 9 components to TWSA are very dependent on the model and basin. A major contributor to the 10 TWSA is the anomaly of total column soil moisture content (SMCA) for CLM4.0 and Noah-MP 11 or groundwater storage anomaly (GWSA) for CLSM-F2.5 although other components such as 12 the anomaly of snow water equivalent (SWEA) also play some role. For each individual water 13 storage component, the models are able to capture broad features such as monthly and 14 interannual variability. However, there are large inter-model differences and quantitative 15 uncertainties in this study. Therefore, it should be thought of as a preliminary synthesis and 16 analysis.

58 GEOSCIENCES↗
DOE OSTI2023

Dataset Repository for Investigating Suicide Risk Using Social and Environmental Determinants of Health

Suicide is frequently modeled as a function of genetics and environment, where the latter refers to factors other than direct biological consequences, such as air quality, financial level, social connectivity, transportation and food access, and homelessness status. According to the World Health Organization, clean air, a stable climate, adequate water, sanitation and hygiene, safe chemical use, radiation protection, healthy and safe workplaces, sound agricultural practices, health-supportive cities and built environments, and a preserved natural environment are all prerequisites for good health. Understanding the relationships between these determinants and mental health outcomes requires standardized data that can be included in healthcare programs and health outcome models. There is a wealth of publicly available data on social and environmental factors provided by various US organizations that can benefit the design of health care systems and public health interventions, as well as improve our comprehension of factors that impact health. Such information would not only help improve the understanding of individual and community risk but also identify new risk factors that have not previously been therapeutically targeted, especially in terms of their impact on mental health. However, curating and standardizing such datasets is challenging because they are often recorded at numerous geographical and temporal resolutions and with varying spatial and temporal granularities. To address this challenge, we launched an endeavor in conjunction with the Veterans Health Administration to collect publicly available socioeconomic and environmental determinants of health statistics in the US. In this manuscript, we describe a social and environmental determinants of health (SEDH) datasets repository, data curation documentation, and a pipeline framework for data generation; This effort started in 2020, when we began constructing a scalable pipeline to automate the download, extraction, preparation, analysis, and production of datasets. These datasets have been made available to the VHA and may be shared upon agreement with collaborating organizations.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Low-altitude remote sensing dataset of DEM and RGB mosaic for AB corridor on July 13 2013 and L2 corridor on July 21 2013, Utqiagvik (Barrow), Alaska

Photogrammetry and topography data were acquired in July 2023 along a 475 m long, 20 m wide corridor (named L2 or Z0) and a 500 m long, 40 m wide corridor (AB), both covering various polygon types within the Barrow Environmental Observatory (BEO) on the Alaskan Arctic Coastal Plain, approximately 4 miles from the Beaufort Sea near Utqiaġvik, Alaska. This dataset was collected to improve the understanding of landscape organization and obtain a high-resolution digital surface model to investigate co-variability between above- and below-ground structure. The reference list provided in this archive indicates studies using this dataset. The photogrammetry data were acquired using an unoccupied aerial vehicle (UAV) (specifically, a kite) and were used to generate a digital elevation model and an RGB mosaic. A real-time kinematic (RTK) GPS was used to survey ground control points for the aerial imagery. The processes datasets are provided in geotiff format with a UTM coordinate system. The dataset contains 1 *.csv metadata files, and 6 *.tif files. 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 OSTI2016

Regionalization of land use impact models for life cycle assessment: Recommendations for their use on the global scale and their applicability to Brazil

Life Cycle Assessment (LCA) is the main technique for evaluate the environmental impacts of product life cycles. A major challenge in the field of LCA is spatial and temporal differentiation in Life Cycle Impact Assessment (LCIA) methods, especially impacts resulting from land occupation and land transformation. Land use characterization modeling has advanced considerably over the last two decades and many approaches have recently included crucial aspects such as geographic differentiation. Nevertheless, characterization models have so far not been systematically reviewed and evaluated to determine their applicability to South America. Given that Brazil is the largest country in South America, this paper analyzes the main international characterization models currently available in the literature, with a view to recommending regionalized models applicable on a global scale for land use life cycle impact assessments, and discusses their feasibility for regionalized assessment in Brazil. The analytical methodology involves classification based on the following criteria: midpoint/endpoint approach, scope of application, area of data collection, biogeographical differentiation, definition of recovery time and reference situation; followed by an evaluation of thirteen scientific robustness and environmental relevance subcriteria. The results of the scope of application are distributed among 25% of the models developed for the European context, and 50% have a global scope. There is no consensus in the literature about the definition of parameters such biogeographical differentiation and reference situation, and our review indicates that 35% of the models use ecoregion division while 40% use the concept of potential natural vegetation. Four characterization models show high scores in terms of scientific robustness and environmental relevance. These models are recommended for application in land use life cycle impact assessments, and also to serve as references for the development or adaptation of regional methodological procedures for Brazil. - Highlights: • A discussion is made on performing regionalized impact assessments using spatial differentiation in LCA. • A review is made of 20 characterization models for land use impacts in Life Cycle Impact Assessment. • Four characterization models are recommended according to different land use impact pathways for application in Brazil.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Thermal modeling of directed energy deposition additive manufacturing using graph theory

Purpose: The purpose of this paper is to develop, apply and validate a mesh-free graph theory–based approach for rapid thermal modeling of the directed energy deposition (DED) additive manufacturing (AM) process. Design/methodology/approach: Here, the authors develop a novel mesh-free graph theory–based approach to predict the thermal history of the DED process. Subsequently, the authors validated the graph theory predicted temperature trends using experimental temperature data for DED of titanium alloy parts (Ti-6Al-4V). Temperature trends were tracked by embedding thermocouples in the substrate. The DED process was simulated using the graph theory approach, and the thermal history predictions were validated based on the data from the thermocouples. Findings: The temperature trends predicted by the graph theory approach have mean absolute percentage error of approximately 11% and root mean square error of 23°C when compared to the experimental data. Moreover, the graph theory simulation was obtained within 4 min using desktop computing resources, which is less than the build time of 25 min. By comparison, a finite element–based model required 136 min to converge to similar level of error. Research limitations/implications: This study uses data from fixed thermocouples when printing thin-wall DED parts. In the future, the authors will incorporate infrared thermal camera data from large parts. Practical implications: The DED process is particularly valuable for near-net shape manufacturing, repair and remanufacturing applications. However, DED parts are often afflicted with flaws, such as cracking and distortion. In DED, flaw formation is largely governed by the intensity and spatial distribution of heat in the part during the process, often referred to as the thermal history. Accordingly, fast and accurate thermal models to predict the thermal history are necessary to understand and preclude flaw formation. Originality/value: This paper presents a new mesh-free computational thermal modeling approach based on graph theory (network science) and applies it to DED. The approach eschews the tedious and computationally demanding meshing aspect of finite element modeling and allows rapid simulation of the thermal history in additive manufacturing. Although the graph theory has been applied to thermal modeling of laser powder bed fusion (LPBF), there are distinct phenomenological differences between DED and LPBF that necessitate substantial modifications to the graph theory approach.

42 ENGINEERING↗
DOE OSTI2022

Summary of LANL Critical Benchmark Comparison Study and Revisions for Cases Involving HEU, LEU, MIX, and Pu

This report documents results obtained for revisions made to cases involving Highly Enriched Uranium (HEU), Intermediate Enriched Uranium (IEU), a mixture of Pu and Uranium (MIX), as well as Pu cases. A previous summary of revisions for HEU an Pu cases was reported and additional investigations into four cases originally presented therein uncovered further revisions which led to better agreement with other transport codes, those cases are updated in this report. The summary of all cases reported in Reference 2 is updated in this report. In addition, a previous summary of revisions for LEU and MIX was reported, a summary of those revisions in reproduced in this report for a comprehensive summary of changes to benchmarks beginning in fiscal year 2020 to current date. The report focuses on the changes made to LANL benchmarks modeled with MCNP6 using ENDF/B-VII.1 nuclear data that appeared to have discrepant results when compared with results of other codes. Feedback was used to pinpoint review of benchmark input files and to revise them when necessary. This report documents the results of review and revision of specific benchmarks highlighted as possibly discrepant in the comparison study. In addition, there is an effort tied to this work involving collaboration between LANL XCP and NCS Divisions in the development of a shared review/revision procedure and use of a new benchmark repository. LANL has a benchmark library of critical experiments from the International Criticality Safety Benchmark Evaluation Project (ICSBEP) Handbook modeled for use with MCNP. This collection is now over 1100 benchmarks, referred to as the Whisper-1.1 library because it is used with the sensitivity/uncertainty package, Whisper, which supports nuclear criticality safety validation and is released with MCNP6.2. The collection, originally created several decades ago, is a combination of smaller collections, which has been revised and expanded, by various groups at LANL over the years. The original authors are no longer at the laboratory and little formal documentation of review and revision of these benchmarks exists today. A branch of the benchmark collection was already the subject of a formal review undertaken by the LANL NCS Division and expanded to include XCP Division.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Self-similar Reynolds-averaged mechanical–scalar turbulence models for Rayleigh–Taylor, Richtmyer–Meshkov, and Kelvin–Helmholtz instability-induced mixing in the small Atwood number limit

Analytical self-similar solutions to two-, three-, and four-equation Reynolds-averaged mechanical–scalar turbulence models describing incompressible turbulent Rayleigh–Taylor, Richtmyer–Meshkov, and Kelvin–Helmholtz instability-induced mixing in planar geometry are derived in the small Atwood number (Boussinesq) limit. The models are based on the turbulent kinetic energy K and its dissipation rate ε, together with the scalar (heavy-fluid mass fraction) variance S and its dissipation rate Χ modeled either differentially or algebraically. The models allow for a simultaneous description of mechanical and scalar mixing, i.e., mixing layer growth and molecular mixing, respectively. Mixing layer growth parameters and other physical observables relevant to each instability are obtained explicitly as functions of the model coefficients. The turbulent fields are also expressed in terms of the model coefficients, with their temporal power-law scalings obtained by requiring that the self-similar equations are explicitly time-independent. The model calibration methodology is described and discussed. Expressions for a subset of the various physical observables are used to calibrate each of the two-, three-, and four-equation models, such that the self-similar solutions are consistent with experimental and numerical simulation data corresponding to these values of the observables and to specific canonical Rayleigh–Taylor, Richtmyer–Meshkov, and Kelvin–Helmholtz turbulent flows. A calibrated four-equation model is then used to reconstruct the mean and turbulent fields, and late-time turbulent equation budgets for each instability-induced flow across the mixing layer. The reference solutions derived here can provide systematic calibrations and better understanding of mechanical–scalar turbulence models and their predictions for instability-induced turbulent mixing in the very large Reynolds number limit.

42 ENGINEERING↗
DOE OSTI2019

Review, Evaluation, and Directions for Gene-Targeted Assembly for Ecological Analyses of Metagenomes

Shotgun metagenomics has greatly advanced our understanding of microbial communities over the last decade. Metagenomic analyses often include assembly and genome binning, computationally daunting tasks especially for big data from complex environments such as soil and sediments. In many studies, however, only a subset of genes and pathways involved in specific functions are of interest; thus, it is not necessary to attempt global assembly. In addition, methods that target genes can be computationally more efficient and produce more accurate assembly by leveraging rich databases, especially for those genes that are of broad interest such as those involved in biogeochemical cycles, biodegradation, and antibiotic resistance or used as phylogenetic markers. Here, we review six gene-targeted assemblers with unique algorithms for extracting and/or assembling targeted genes: Xander, MegaGTA, SAT-Assembler, HMM-GRASPx, GenSeed-HMM, and MEGAN. We tested these tools using two datasets with known genomes, a synthetic community of artificial reads derived from the genomes of 17 bacteria, shotgun sequence data from a mock community with 48 bacteria and 16 archaea genomes, and a large soil shotgun metagenomic dataset. We compared assemblies of a universal single copy gene (rplB) and two N cycle genes (nifH and nirK). We measured their computational efficiency, sensitivity, specificity, and chimera rate and found Xander and MegaGTA, which both use a probabilistic graph structure to model the genes, have the best overall performance with all three datasets, although MEGAN, a reference matching assembler, had better sensitivity with synthetic and mock community members chosen from its reference collection. Also, Xander and MegaGTA are the only tools that include post-assembly scripts tuned for common molecular ecology and diversity analyses. Additionally, we provide a mathematical model for estimating the probability of assembling targeted genes in a metagenome for estimating required sequencing depth.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Comparing projections of industrial energy demand and greenhouse gas emissions in long-term energy models

The industry sector consumes more energy and emits more greenhouse gas (GHG) emissions than any other end-use sector. Integrated assessment models (IAMs) and energy system models have been widely used to evaluate climate policy at a global level, and include a representation of industrial energy use. In this study, the projected industrial energy use and accompanying GHG emissions, as well as the model structure of multiple long-term energy models are compared. The models show varying degrees to which energy consumption is decoupled from GDP growth in the future. In all models, the sector remains mostly (>50%) reliant on fossil energy through 2100 in a reference scenario (i.e., absent emissions mitigation policies), though there is significant divergence in the projected ability to switch to alternative fuels to mitigate GHG emissions. Among the set analyzed here, the more technologically detailed models tend to have less capacity for switching from fossil fuels to electricity. This highlights the importance of understanding of economy-wide mitigation responses and costs as an area for future improvement. Analyzing industry subsector material and energy use details can improve the ability to interpret results, and provide insight in feasibility of how emissions reduction can be achieved.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2025

Efficient wind farm layout optimization with the FLOWERS AEP model and analytic gradients

Wind farm layout optimization (WFLO) studies often aim to maximize the annual energy production (AEP) of a wind farm by choosing an arrangement of turbines that minimizes wake interactions. One way to reduce the cost of WFLO studies is by using more computationally efficient AEP models. The cost of standard AEP modeling approaches, based on the numerical integration of low-fidelity engineering wake models, scales poorly with the number of simulated discrete wind conditions. A second way to reduce cost when using a gradient-based algorithm is to supply exact gradient information instead of finite-difference estimates. However, analytical functions for the derivatives of AEP with respect to turbine positions are not always available in the conventional modeling approach. FLOWERS is a computationally inexpensive, analytical model for wind farm AEP that is specifically developed for WFLO applications. In this paper, we analyze the performance of the FLOWERS AEP model with analytic gradients in a layout optimization study compared with a reference optimization framework across three wind farm case studies. We find that the FLOWERS-based approach reduces computation time by a factor of 50–4000 and improves optimal AEP by about 0.3% with less than half of the variability in AEP across instances with randomized initial conditions. We also find the optimal layouts to be insensitive to model parameter tuning, making FLOWERS-based layout optimization a streamlined, user-friendly approach.

17 WIND ENERGY↗
DOE OSTI2025

Modeling Losses in a Three Electrode System Towards Fast Charge Control

In this work we demonstrate the applicability of a versatile separator-reference mounted electrode in a three-electrode setup to accurately capture the primary current pathway in the battery cell during operation, calibrate a porous electrode model to the individual anode and cathode potential signals, and assign the various resistances to electrochemical phenomena in the battery cell. This calibrated electrochemical model is validated using continuous rate discharges associated with highway driving scenarios in an electric vehicle, and in turn utilized to predict the local anode potential and proximity to lithium plating onset. Finally, we demonstrate the strategy associated with utilization of the model to estimate constant anode potential charging during fast charge scenarios at various rates and starting conditions as a future look to fast charge calibration development and controls.

Garrick, Taylor R. (ORCID:0000000322518129)↗
DOE OSTI2023

Performance efficient macromolecular mechanics via sub-nanometer shape based coarse graining

Dimensionality reduction via coarse grain modeling is a valuable tool in biomolecular research. For large assemblies, ultra coarse models are often knowledge-based, relying on a priori information to parameterize models thus hindering general predictive capability. Here, we present substantial advances to the shape based coarse graining (SBCG) method, which we refer to as SBCG2. SBCG2 utilizes a revitalized formulation of the topology representing network which makes high-granularity modeling possible, preserving atomistic details that maintain assembly characteristics. Further, we present a method of granularity selection based on charge density Fourier Shell Correlation and have additionally developed a refinement method to optimize, adjust and validate high-granularity models. We demonstrate our approach with the conical HIV-1 capsid and heteromultimeric cofilin-2 bound actin filaments. Our approach is available in the Visual Molecular Dynamics (VMD) software suite, and employs a CHARMM-compatible Hamiltonian that enables high-performance simulation in the GPU-resident NAMD3 molecular dynamics engine.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Extremum-Seeking-Based Ultra-local Model Predictive Control and Its Application to Electric Motor Speed Regulation

Electric vehicle (EV) market is rapidly expanding. As a critical component of EV, an electric motor needs to accurately follow a reference speed signal while respecting the electrical current constraint for safety. Those requirements are usually formulated as a model predictive control (MPC) problem. However, the performance of traditional model-based MPC depends on the accuracy of the system model, which may not always be guaranteed in reality. Therefore, we utilize a data-driven, model-free predictive control strategy, called ultra-local MPC (ULMPC), to control the speed of an electric motor. To further enhance the control performance of ULMPC, we employ the extremum-seeking control (ESC) to tune the control gain of the ULMPC online. Simulation and hardware experiments demonstrate the enhancement of the extremum-seeking-based ULMPC over a constant-gain ULMPC.

Zhou, Yujing↗
DOE OSTI2021

Parametric study of solid-solid translucent phase change materials in building windows

Thermal energy storage and solar radiation management are crucial to improve the sustainability and energy efficiency of buildings. Compared with the implementation of phase change materials (PCMs) in opaque components, the energy saving potential of incorporating PCMs in transparent glazing windows is much less studied and not well understood. Here we present a comprehensive parametric study of novel PCM windows for building energy saving with a focus on optimizing and quantitatively distinguishing the contributions from the optical and thermal properties of the PCM, which is particularly useful for the design of solid-solid PCM windows. We investigate a reference commercial office building using EnergyPlus by developing an equivalent model of our PCM window that is compatible with EnergyPlus's modeling capabilities. Compared with a clear-clear double-pane window, the integration of 3 mm solid-solid PCMs with optimal properties in warm, mixed, and cold climates can respectively save up to 17.2%, 14.0%, and 5.8% energy for the HVAC (heating, ventilation, and air conditioning) system, and 9.4%, 6.7%, and 3.2% energy for the whole building. We also demonstrate that these energy savings are most sensitive to the solar absorptance of PCMs for all three climates. The optimal transition temperature varies with climate and is related to the climate and solar radiation heat gain. Other issues are also briefly discussed, such as hysteresis, window orientations, and the effect of interior lighting. Finally, although the optimal PCM windows show energy saving performance comparable with low-emissivity windows, the PCM windows provide a unique advantage in terms of shifting HVAC loads which can provide benefits to the electrical grid.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2022

DECOVALEX-2019: An international collaboration for advancing the understanding and modeling of coupled thermo-hydro-mechanical-chemical (THMC) processes in geological systems

The DECOVALEX Project is an international research collaboration for advancing the understanding and modeling of coupled thermo-hydro-mechanical-chemical (THMC) processes in geological systems. DECOVALEX stands for “DEvelopment of COupled Models and VALidation against EXperiments”. The creation of this international initiative, now running for almost 30 years, was motivated by the recognition that prediction of these coupled effects is an essential part of the performance and safety assessment of geologic disposal systems for radioactive waste and spent nuclear fuel, and also for a range of other sub-surface engineering activities. DECOVALEX emphasizes joint analysis and comparative modeling of state-of-the-art field and laboratory experiments, across a range of host rock options and repository designs. Participating research teams are from radioactive waste management organizations, national research institutes, regulatory agencies, universities, and consulting groups, providing a wide range of perspectives and solutions to these complex problems. The most recent phase of the DECOVALEX Project, here referred to as DECOVALEX-2019, started in 2016 and ended in 2019. Modeling teams from 13 international partner organizations participated in the comparative evaluation of seven modeling tasks involving complex field and/or laboratory experiments. Furthermore, this Virtual Special Issue on DECOVALEX-2019 provides an in-depth overview of these collaborative research efforts and how these have advanced the state-of-the-art of understanding and modeling coupled THMC processes.

58 GEOSCIENCES↗
DOE OSTI2022

Austenitic parent grain reconstruction in martensitic steel using deep learning

In this work we develop a deep convolutional architecture to estimate the prior austenite structure from observed martensite electron backscatter diffraction micrographs. A novel data augmentation strategy randomizes the global reference coordinate system which makes it possible to train our model from only four micrographs. The model is much faster than algorithmic approaches and generalizes well when applied to micrographs of a different material. Empirical evidence suggests the efficacy of the model depends on the scale of the microstructure and receptive field of the vision model. Furthermore, this work demonstrates that modern computer vision approaches are well suited for capturing complex spatial-orientation patterns present in orientation imaging micrographs.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Learning perturbation-inducible cell states from observability analysis of transcriptome dynamics

Abstract A major challenge in biotechnology and biomanufacturing is the identification of a set of biomarkers for perturbations and metabolites of interest. Here, we develop a data-driven, transcriptome-wide approach to rank perturbation-inducible genes from time-series RNA sequencing data for the discovery of analyte-responsive promoters. This provides a set of biomarkers that act as a proxy for the transcriptional state referred to as cell state. We construct low-dimensional models of gene expression dynamics and rank genes by their ability to capture the perturbation-specific cell state using a novel observability analysis. Using this ranking, we extract 15 analyte-responsive promoters for the organophosphate malathion in the underutilized host organism Pseudomonas fluorescens SBW25. We develop synthetic genetic reporters from each analyte-responsive promoter and characterize their response to malathion. Furthermore, we enhance malathion reporting through the aggregation of the response of individual reporters with a synthetic consortium approach, and we exemplify the library’s ability to be useful outside the lab by detecting malathion in the environment. The engineered host cell, a living malathion sensor, can be optimized for use in environmental diagnostics while the developed machine learning tool can be applied to discover perturbation-inducible gene expression systems in the compendium of host organisms.

59 BASIC BIOLOGICAL SCIENCES↗