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At least 1,297 records · Page 72
All sourcesNASA NTRSDOE OSTI
NASA NTRS2012

Method to Enhance the Operation of an Optical Inspection Instrument Using Spatial Light Modulators

For many aspheric and freeform optical components, existing interferometric solutions require a custom computer-generated hologram (CGH) to characterize the part. The overall objective of this research is to develop hardware and a procedure to produce a combined, dynamic, Hartmann/ Digital Holographic interferometry inspection system for a wide range of advanced optical components, including aspheric and freeform optics. This new instrument would have greater versatility and dynamic range than currently available measurement systems. The method uses a spatial light modulator to pre-condition wavefronts for imaging, interferometry, and data processing to improve the resolution and versatility of an optical inspection instrument. Existing interferometers and Hartmann inspection systems have either too small a dynamic range or insufficient resolution to characterize conveniently unusual optical surfaces like aspherical and freeform optics. For interferometers, a specially produced, computer-generated holographic optical element is needed to transform the wavefront to within the range of the interferometer. A new hybrid wavefront sensor employs newly available spatial light modulators (SLMs) as programmable holographic optical elements (HOEs). The HOE is programmed to enable the same instrument to inspect an optical element in stages, first by a Hartmann measurement, which has a very large dynamic range but less resolution. The first measurement provides the information required to precondition a reference wave that avails the measurement process to the more precise phase shifting interferometry. The SLM preconditions a wavefront before it is used to inspect an optical component. This adds important features to an optical inspection system, enabling not just wavefront conditioning for null testing and dynamic range extension, but also the creation of hybrid measurement procedures. This, for example, allows the combination of dynamic digital holography and Hartmann sensing procedures to cover a virtually unlimited dynamic range with high resolution. Digital holography technology brings all of the power and benefits of digital holographic interferometry to the requirement, while Hartmann-type wavefront sensors bring deflectometry technologies to the solution. The SLM can be used to generate arbitrary wavefronts in one leg of the interferometer, thereby greatly simplifying its use and extending its range. The SLM can also be used to modify the system into a dynamic Shack-Hartmann system, which is useful for optical components with large amounts of slope. By integrating these capabilities into a single instrument, the system will have tremendous flexibility to measure a variety of optical shapes accurately.

Trolinger, James↗
NASA NTRS1976

The use of spatial characteristics for the improvement of multispectral classification of remotely sensed data

Two techniques for the classification of multispectral remotely sensed data - the image processing technique of texture features, which is modeled after the human visual system, and the ECHO (Extraction and Classification of Homogeneous Objects) numerical technique - are examined. These two spatial analysis techniques are compared using Landsat imagery of an area of Indiana as an example, and it is found that the numerical approach is superior in classification accuracy and more efficient computationally.

Wiersma, D. J.↗
NASA NTRS2004

Ecosystem Impacts of Woody Encroachment In Texas: A Spatial Analysis Using AVIRIS

Woody encroachment, the increase of woody plant density relative to herbaceous vegetation, has been documented in drylands of Texas as well as worldwide (Archer 1994, Harrington and Harman 1995, Moleele et al. 2002). Over-grazing, fire suppression and climate change are implicated in the shift from open grasslands to ecosystems now populated by trees and shrubs (Scholes and Archer 1997, Archer et al. 2001), such as Prosopis glandulosa var. glandulosa (honey mesquite) in north Texas (Teague et al. 1997, Ansley et al. 2001, Asner et al. 2003a). Several studies have examined changes in ecosystem properties accompanying woody vegetation encroachment in the Southwest U.S., with research focused on increases in plant and soil carbon (C) and nitrogen (N) stores (Hoffman and Jackson 2000, Asner et al. 2003a), isotopic shifts in these pools (Boutton 1999, Archer et al. 2001), and increases in N cycling rates (Rundel et al. 1982, Hibbard et al. 2001). However, little is known regarding the impact of woody encroachment on N trace gas emissions from dryland regions such as Texas. NOx is produced in the soil during the processes of nitrification and denitrification (Firestone and Davidson 1989). The total N efflux from soils is most directly influenced by the internal cycling of N, which at a regionalscale, is controlled by the inputs and availability of N from vegetation via litterfall and subsequent decomposition (Robertson et al. 1989). Although plot-scale studies are critical to understanding controls over N oxide emissions, regionalization of the measurements is impeded by spatial variation in the factors contributing most to N cycling processes: soil properties (affecting soil moisture regimes and N stocks) and vegetation cover (affecting litter inputs and N uptake). While broad patterns in ecosystem structure and vegetation composition co-vary with general patterns of trace gas emissions (Matson 1997), there is no easily measured index of N availability that can be applied for regional-scale studies of N oxide fluxes. Remote sensing is arguably the only approach available to develop a spatially-explicit understanding of ecosystem processes. More specifically, remotely detectable spatial patterns in the distal controls over soil N properties, such as vegetation cover, land use and soil type (Robertson et al. 1989), should be exploited for regional studies of N oxide emissions. The woody encroachment phenomenon provides an opportunity to test the strength of the relationship between N oxide emissions and those factors controlling the fluxes that can be remotely measured. If such linkages can be firmly established, and if the spatial pattern of distal controls is relevant, then the combination of field measurements and remote sensing offers to improve regional-scale N oxide estimates. The paper presents the utility of linking field based sampling of soil NOx emissions with very high resolution remote sensing estimates of woody vegetation cover from the NASA AVIRIS, Airborne Visible-Infrared Imaging Spectrometer (Green et al. 1998, Asner and Green 2001) and automated spectral mixture analysis (Asner and Lobell 2000, Asner and Heidebrecht 2002) that provide a means to spatially extrapolate soil NOx emissions to the regional scale.

Martin, Roberta E.↗
DOE OSTI2022

Robust two-colour pyrometry uncertainty analysis to acquire spatially-resolved measurements

Two-colour pyrometry (2CP) has been used over several decades to study engine-relevant combustion processes, but results are generally regarded as qualitative or semi-quantitative. In many current 2CP systems, large measurement errors are introduced by parallax because the two measured wavelengths are not from the same line of sight. Here this work presents a spatially-resolved 2CP system with the objective of quantifying and reducing measurement uncertainty. An optical setup that eliminates parallax in 2CP is used together with pixel-by-pixel calibration of the camera sensor to increase measurement accuracy. Primary uncertainty terms are identified, and an error propagation analysis is performed to compute uncertainties in the final results of soot temperature, soot concentration parameter, KL, and soot mass. These methodologies are applied to investigate an auto-igniting fuel spray in a constant pressure flow rig at diesel-like conditions of high ambient pressure and temperature. Results show bias uncertainty of around 200 K (≈10%) for temperature and about 40%–60% for KL. High uncertainty was found to occur on the diffusion flame front where both optical thickness and soot concentrations are small. However, these uncertain measurement zones with relatively low soot concentrations contribute minimally to the total soot mass present in the reacting jet during the temporal evolution of the flame.

42 ENGINEERING↗
NASA NTRS1993

Plasma dynamics driven by finite-width current filament and KV potential drops in ionosphere-magnetosphere coupling

We have simulated the plasma dynamics of a quasi-two-dimensional current filament in ionosphere-magnetosphere coupling. The simulation consists of a set of one-dimensional flux tube simulations with different imposed time-dependent, field-aligned currents. The dynamical interactions of the individual current filaments with the ionospheric and magnetospheric plasma generate kV field-aligned potential drops along the field lines, and the side-by-side display exhibits the evolution of the implied potential structure in the horizontal direction. The primary cross-field motion produced by the horizontal E-field (ExB drift) is perpendicular to both of the significant spatial directions, and is thus ignorable in this geometry. The effects of other cross-field drict processes are discussed. The simulation thus provides insight into the dynamical evolution of 2D potential structures driven by an imposed finite-width field-aligned current profile. Spatial and temporal variation of other plasma parameters (temperatures, density, etc.) that are determined primarily by parallel transport effects are also displayed.

Ganguli, Supriya B.↗
NASA NTRS2004

Experimental Test-Bed for Intelligent Passive Array Research

This document describes the test-bed designed for the investigation of passive direction finding, recognition, and classification of speech and sound sources using sensor arrays. The test-bed forms the experimental basis of the Intelligent Small-Scale Spatial Direction Finder (ISS-SDF) project, aimed at furthering digital signal processing and intelligent sensor capabilities of sensor array technology in applications such as rocket engine diagnostics, sensor health prognostics, and structural anomaly detection. This form of intelligent sensor technology has potential for significant impact on NASA exploration, earth science and propulsion test capabilities. The test-bed consists of microphone arrays, power and signal distribution modules, web-based data acquisition, wireless Ethernet, modeling, simulation and visualization software tools. The Acoustic Sensor Array Modeler I (ASAM I) is used for studying steering capabilities of acoustic arrays and testing DSP techniques. Spatial sound distribution visualization is modeled using the Acoustic Sphere Analysis and Visualization (ASAV-I) tool.

Solano, Wanda M.↗
DOE OSTI2021

Two-phase accurate multiplexed structured image capture (2pAc-MUSIC)

Multiplexed Structural Image Capture (MUSIC) technique uses modulation of light from a scene prior to imaging to encode the temporal evolution of target into spatial frequency shifts, with each shift corresponding to a unique time and resulting in individual distinct snapshots. Computational-processing of the multiplexed single-shot image can recover the nanosecond-resolution scene evolution. One of the limitations is the loss of spatial resolution of the recovered image due to limitations of the low-pass spatial frequency filtering depth. Here we demonstrated that two images with complementary spatial phases can be used to enhance the spatial resolutions. For this application, 2 Phase Accurate (2pAc)-MUSIC is implemented that a scene is encoded with two complementary phases. The increased spatial information captured reduces the lower frequency noise in the Fourier domain found in single-phase MUSIC. A recovery algorithm combines the 180-degree spatial frequency shifted images into a single scene and applies a spatial filter in the Fourier domain that has a larger depth than previously possible to achieve a scene with increased spatial resolution. The 2pAc-MUSIC can effectively enhance the spatial resolution by removing the overlapping zero-order spatial frequencies.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Self-Supervised Cloud Classification

Abstract Low-level marine clouds play a pivotal role in Earth’s weather and climate through their interactions with radiation, heat and moisture transport, and the hydrological cycle. These interactions depend on a range of dynamical and microphysical processes that result in a broad diversity of cloud types and spatial structures, and a comprehensive understanding of cloud morphology is critical for continued improvement of our atmospheric modeling and prediction capabilities moving forward. Deep learning has recently accelerated our ability to study clouds using satellite remote sensing, and machine learning classifiers have enabled detailed studies of cloud morphology. A major limitation of deep learning approaches to this problem, however, is the large number of hand-labeled samples that are required for training. This work applies a recently developed self-supervised learning scheme to train a deep convolutional neural network (CNN) to map marine cloud imagery to vector embeddings that capture information about mesoscale cloud morphology and can be used for satellite image classification. The model is evaluated against existing cloud classification datasets and several use cases are demonstrated, including training cloud classifiers with very few labeled samples, interrogation of the CNN’s learned internal feature representations, cross-instrument application, and resilience against sensor calibration drift and changing scene brightness. The self-supervised approach learns meaningful internal representations of cloud structures and achieves comparable classification accuracy to supervised deep learning methods without the expense of creating large hand-annotated training datasets. Significance Statement Marine clouds heavily influence Earth’s weather and climate, and improved understanding of marine clouds is required to improve our atmospheric modeling capabilities and physical understanding of the atmosphere. Recently, deep learning has emerged as a powerful research tool that can be used to identify and study specific marine cloud types in the vast number of images collected by Earth-observing satellites. While powerful, these approaches require hand-labeling of training data, which is prohibitively time intensive. This study evaluates a recently developed self-supervised deep learning method that does not require human-labeled training data for processing images of clouds. We show that the trained algorithm performs competitively with algorithms trained on hand-labeled data for image classification tasks. We also discuss potential downstream uses and demonstrate some exciting features of the approach including application to multiple satellite instruments, resilience against changing image brightness, and its learned internal representations of cloud types. The self-supervised technique removes one of the major hurdles for applying deep learning to very large atmospheric datasets.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2008

Hyperspectral Fluorescence and Reflectance Imaging Instrument

The system is a single hyperspectral imaging instrument that has the unique capability to acquire both fluorescence and reflectance high-spatial-resolution data that is inherently spatially and spectrally registered. Potential uses of this instrument include plant stress monitoring, counterfeit document detection, biomedical imaging, forensic imaging, and general materials identification. Until now, reflectance and fluorescence spectral imaging have been performed by separate instruments. Neither a reflectance spectral image nor a fluorescence spectral image alone yields as much information about a target surface as does a combination of the two modalities. Before this system was developed, to benefit from this combination, analysts needed to perform time-consuming post-processing efforts to co-register the reflective and fluorescence information. With this instrument, the inherent spatial and spectral registration of the reflectance and fluorescence images minimizes the need for this post-processing step. The main challenge for this technology is to detect the fluorescence signal in the presence of a much stronger reflectance signal. To meet this challenge, the instrument modulates artificial light sources from ultraviolet through the visible to the near-infrared part of the spectrum; in this way, both the reflective and fluorescence signals can be measured through differencing processes to optimize fluorescence and reflectance spectra as needed. The main functional components of the instrument are a hyperspectral imager, an illumination system, and an image-plane scanner. The hyperspectral imager is a one-dimensional (line) imaging spectrometer that includes a spectrally dispersive element and a two-dimensional focal plane detector array. The spectral range of the current imaging spectrometer is between 400 to 1,000 nm, and the wavelength resolution is approximately 3 nm. The illumination system consists of narrowband blue, ultraviolet, and other discrete wavelength light-emitting-diode (LED) sources and white-light LED sources designed to produce consistently spatially stable light. White LEDs provide illumination for the measurement of reflectance spectra, while narrowband blue and UV LEDs are used to excite fluorescence. Each spectral type of LED can be turned on or off depending on the specific remote-sensing process being performed. Uniformity of illumination is achieved by using an array of LEDs and/or an integrating sphere or other diffusing surface. The image plane scanner uses a fore optic with a field of view large enough to provide an entire scan line on the image plane. It builds up a two-dimensional image in pushbroom fashion as the target is scanned across the image plane either by moving the object or moving the fore optic. For fluorescence detection, spectral filtering of a narrowband light illumination source is sometimes necessary to minimize the interference of the source spectrum wings with the fluorescence signal. Spectral filtering is achieved with optical interference filters and absorption glasses. This dual spectral imaging capability will enable the optimization of reflective, fluorescence, and fused datasets as well as a cost-effective design for multispectral imaging solutions. This system has been used in plant stress detection studies and in currency analysis.

Ryan, Robert E.↗
DOE OSTI2021

Efficient interlayer electron transfer in a MoTe 2 /WS 2 /MoS 2 trilayer heterostructure

Electron transfer and carrier dynamics in MoTe 2 /WS 2 /MoS 2 trilayer heterostructures are investigated by transient absorption and photoluminescence measurements. Monolayer flakes of MoTe 2 , WS 2 , and MoS 2 are obtained by mechanical exfoliation from their bulk crystals and are used to fabricate the heterostructures by a dry-transfer technique. Here, photoluminescence spectroscopic measurements indicate that the recombination of the MoS 2 and WS 2 intralayer excitons is significantly suppressed in the heterostructure, illustrating the efficient interlayer charge transfer processes. Layer-selective time-resolved differential reflectance measurements show that the electrons excited in MoTe 2 can transfer to MoS 2 within 0.3 ps. The transferred electrons show a long lifetime of several hundred picoseconds due to their slow recombination with the spatially separated holes that reside in MoTe 2 . Furthermore, the charge transfer and recombination processes are weakly dependent on the injected carrier density. These results demonstrate the feasibility of constructing van der Waals multilayer heterostructures involving the infrared-sensitive MoTe 2 with emergent properties and provide important information to quantify the performance of MoTe 2 - based devices.

2D materials↗
NASA NTRSDate not supplied

Characterizing Spatiotemporal Uncertainty in Interpolated Meteorological Data

Interpolated meteorological data invariably contain errors. These errors have structure in time and space, particularly autocorrelation, which can cause the effects of errors to compound when model outputs are aggregated temporally or spatially. One way to account for this uncertainty is with a probabilistic model from which samples can be drawn that are coherent with respect to underlying spatial and temporal covariance structure. This work describes a probabilistic method for spatial interpolation of point-wise meteorological time series. Observational data from weather stations are generally sparse in space and dense in time (but sometimes missing). The method works by projecting time series onto orthogonal basis vectors and spatially interpolating each resulting component independently. Under suitable assumptions, and data transformations to better satisfy those assumptions, Gaussian process regression provides a complete description of the joint predictive distribution over a Gaussian random field. Spatiotemporally coherent realizations are generated as the sum of conditional (spatial) simulations of each orthogonal (temporal) component. Data-derived and generic orthogonal bases are considered. In addition to spatial interpolation, imputation of missing observational data is examined. The method is applied using near-surface air temperature over the Western United States and validated by comparing theoretical versus actual coverage of predictive distributions and analyzing the degree to which spatial and temporal covariance structure is reproduced. Computational considerations, relating to conditional simulation of random fields, are also addressed.

Conor T Doherty↗
NASA NTRS2010

Design Considerations of Polishing Lap for Computer-Controlled Cylindrical Polishing Process

The future X-ray observatory missions, such as International X-ray Observatory, require grazing incidence replicated optics of extremely large collecting area (3 m2) in combination with angular resolution of less than 5 arcsec half-power diameter. The resolution of a mirror shell depends ultimately on the quality of the cylindrical mandrels from which they are being replicated. Mid-spatial-frequency axial figure error is a dominant contributor in the error budget of the mandrel. This paper presents our efforts to develop a deterministic cylindrical polishing process in order to keep the mid-spatial-frequency axial figure errors to a minimum. Simulation studies have been performed to optimize the operational parameters as well as the polishing lap configuration. Furthermore, depending upon the surface error profile, a model for localized polishing based on dwell time approach is developed. Using the inputs from the mathematical model, a mandrel, having conical approximated Wolter-1 geometry, has been polished on a newly developed computer-controlled cylindrical polishing machine. We report our first experimental results and discuss plans for further improvements in the polishing process.

Khan, Gufran S.↗
DOE OSTI2024

Analytical Modeling of Metal Foam Composite Phase Change Materials (PCM) in Thermal Energy Storage Using Asymptotic Analysis

The use of phase change materials (PCMs) for thermal energy storage can release or absorb a significant amount of latent heat during the freezing or melting process, offering a higher energy storage density. One of the main drawbacks of PCMs is their low thermal conductivity, resulting in poor thermal performance. Recent research has attempted to enhance heat transfer and increase the thermal conductivity of PCMs, including the use of metal foams. However, modeling the metal foam composite PCM using conventional methods is computationally expensive. This paper proposes an asymptotic solution for a Stefan-like problem subject to a convective boundary for outward solidification in a hollow cylinder, capable of predicting the freeze-melt cycle of the metal foam composite PCM. Specifically, three temporal regimes and four spatial layers are considered in the asymptotic analysis for each phase change process. The thermal conductivity is calculated by a theoretical three-dimensional tetrakaidecahedron model, while other thermophysical properties are obtained using the method of volume averaging. The results are verified with numerical data and validated against experimental data in the literature. The presented analytical modeling framework could have the potential to be applied to other types of composite PCMs with considerably lower computational costs compared with conventional methods.

analytical model↗
DOE OSTI2021

Spatial Interpolation of Air Pollutant and Meteorological Variables in Central Amazonia

The Amazon Rainforest is highlighted by the global community both for its extensive vegetation cover that constantly suffers the effects of anthropic action and for its substantial biodiversity. This dataset presents data of meteorological variables from the Amazon Rainforest region with a spatial resolution of 0.001° in latitude and longitude, resulting from an interpolation process. The original data were obtained from the GoAmazon 2014/5 project, in the Atmospheric Radiation Measurement (ARM) repository, and then processed through mathematical and statistical methods. The dataset presented here can be used in experiments in the field of Data Science, such as training models for predicting climate variables or modeling the distribution of species.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2000

BOREAS TE-18, 60-m, Radiometrically Rectified Landsat TM Imagery

The BOREAS TE-18 team used a radiometric rectification process to produce standardized DN values for a series of Landsat TM images of the BOREAS SSA and NSA in order to compare images that were collected under different atmospheric conditions. The images for each study area were referenced to an image that had very clear atmospheric qualities. The reference image for the SSA was collected on 02-Sep-1994, while the reference image for the NSA was collected on 2 1 Jun-1995. The 23 rectified images cover the period of 07-Jul-1985 to 18-Sep-1994 in the SSA and 22-Jun-1984 to 09-Jun-1994 in the NSA. Each of the reference scenes had coincident atmospheric optical thickness measurements made by RSS-11. The radiometric rectification process is described in more detail by Hall et al. (1991). The original Landsat TM data were received from CCRS for use in the BOREAS project. Due to the nature of the radiometric rectification process and copyright issues, the full-resolution (30-m) images may not be publicly distributed. However, this spatially degraded 60-m resolution version of the images may be openly distributed and is available on the BOREAS CD-ROM series. After the radiometric rectification processing, the original data were degraded to a 60-m pixel size from the original 30-m pixel size by averaging the data over a 2- by 2-pixel window. The data are stored in binary image-format files. The data files are available on a CD-ROM (see document number 20010000884), or from the Oak Ridge National Laboratory (ORNL) Distributed Activity Archive Center (DAAC).

Hall, Forrest G.↗
NASA NTRS2001

Synthesis of Multispectral Bands from Hyperspectral Data: Validation Based on Images Acquired by AVIRIS, Hyperion, ALI, and ETM+

Multispectral data requirements for Earth science applications are not always studied rigorously studied before a new remote sensing system is designed. A study of the spatial resolution, spectral bandpasses, and radiometric sensitivity requirements of real-world applications would focus the design onto providing maximum benefits to the end-user community. To support systematic studies of multispectral data requirements, the Applications Research Toolbox (ART) has been developed at NASA's Stennis Space Center. The ART software allows users to create and assess simulated datasets while varying a wide range of system parameters. The simulations are based on data acquired by existing multispectral and hyperspectral instruments. The produced datasets can be further evaluated for specific end-user applications. Spectral synthesis of multispectral images from hyperspectral data is a key part of the ART software. In this process, hyperspectral image cubes are transformed into multispectral imagery without changes in spatial sampling and resolution. The transformation algorithm takes into account spectral responses of both the synthesized, broad, multispectral bands and the utilized, narrow, hyperspectral bands. To validate the spectral synthesis algorithm, simulated multispectral images are compared with images collected near-coincidentally by the Landsat 7 ETM+ and the EO-1 ALI instruments. Hyperspectral images acquired with the airborne AVIRIS instrument and with the Hyperion instrument onboard the EO-1 satellite were used as input data to the presented simulations.

Blonksi, Slawomir↗
NASA NTRS1982

A 'user friendly' geographic information system in a color interactive digital image processing system environment

NASA's Eastern Regional Remote Sensing Applications Center (ERRSAC) has recognized the need to accommodate spatial analysis techniques in its remote sensing technology transfer program. A computerized Geographic Information System to incorporate remotely sensed data, specifically Landsat, with other relevant data was considered a realistic approach to address a given resource problem. Questions arose concerning the selection of a suitable available software system to demonstrate, train, and undertake demonstration projects with ERRSAC's user community. The very specific requirements for such a system are discussed. The solution found involved the addition of geographic information processing functions to the Interactive Digital Image Manipulation System (IDIMS). Details regarding the functions of the new integrated system are examined along with the characteristics of the software.

Campbell, W. J.↗
DOE OSTI2025

Meta Biome: a multiscale model integrating agent-based and metabolic networks to reveal spatial regulation in gut mucosal microbial communities

ABSTRACT Mucosal microbial communities (MMCs) are complex ecosystems near the mucosal layers of the gut essential for maintaining health and modulating disease states. Despite advances in high-throughput omics technologies, current methodologies struggle to capture the dynamic metabolic interactions and spatiotemporal variations within MMCs. In this work, we presentMetaBiome, a multiscale model integrating agent-based modeling (ABM), finite volume methods, and constraint-based models to explore the metabolic interactions within these communities. Integrating ABM allows for the detailed representation of individual microbial agents each governed by rules that dictate cell growth, division, and interactions with their surroundings. Through a layered approach—encompassing microenvironmental conditions, agent information, and metabolic pathways—we simulated different communities to showcase the potential of the model. Using ourin-silicoplatform, we explored the dynamics and spatiotemporal patterns of MMCs in the proximal small intestine and the cecum, simulating the physiological conditions of the two gut regions. Our findings revealed how specific microbes adapt their metabolic processes based on substrate availability and local environmental conditions, shedding light on spatial metabolite regulation and informing targeted therapies for localized gut diseases.MetaBiome provides a detailed representation of microbial agents and their interactions, surpassing the limitations of traditional grid-based systems. This work marks a significant advancement in microbial ecology, as it offers new insights into predicting and analyzing microbial communities. IMPORTANCE Our study presents a novel multiscale model that combines agent-based modeling, finite volume methods, and genome-scale metabolic models to simulate the complex dynamics of mucosal microbial communities in the gut. This integrated approach allows us to capture spatial and temporal variations in microbial interactions and metabolism that are difficult to study experimentally. Key findings from our model include the following: (i) prediction of metabolic cross-feeding and spatial organization in multi-species communities, (ii) insights into how oxygen gradients and nutrient availability shape community composition in different gut regions, and (iii) identification of spatiallyregulated metabolic pathways and enzymes inE. coli. We believe this work represents a significant advance in computational modeling of microbial communities and provides new insights into the spatial regulation of gut microbiome metabolism. The multiscale modeling approach we have developed could be broadly applicable for studying other complex microbial ecosystems.

Microbiology↗