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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Vehicle Platooning: An Energy Consumption Perspective

Urban traffic congestion is a chronic problem faced by many cities in the US and worldwide. It results in inefficient infrastructure use as well as increased vehicle fuel consumption and emission levels. Excessive fuel consumptions add extra costs to commuters as well as transportation businesses. Consuming less fuel and thus reducing costs by a single percentage digit can have a significant impact on the balance sheet as well as the protection of the environment. Researchers have developed, and continue to develop, tools and systems to optimize the operations of fleets as well as engines in order to burn less fuel and therefore generate less CO2 emissions. Platooning is one such tool that attempts to maintain relatively small distances (i.e. pre-determined time gap) between consecutive vehicles. It has the potential to increase the capacity of the road as well as reduce the consumed fuel. In this paper, we use a fuel consumption model for internal combustion light-duty vehicles, electric vehicles, hybrid electric vehicles, buses and trucks in order to determine and quantify the effects of platooning on a fleet fuel consumption. The results suggest that a reduction of up to 3%, 3.5%, 4.5 %, 10%, and 15% in fuel consumption can be achieved for internal combustion engine vehicles, hybrid electric vehicles, electric vehicles, buses and trucks.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2022

Frictional properties of Opalinus Clay: influence of humidity, normal stress and grain size on frictional stability

SUMMARY The Opalinus Clay (OPA) is a clay-rich formation considered as a potential host rock for radioactive waste repositories and as a caprock for carbon storage in Switzerland. Its very low permeability (10−19 to 10−21 m2) makes it a potential sealing horizon, however the presence of faults that may be activated during the lifetime of a repository project can compromise the long-term hydrological confinement, and lead to mechanical instability. Here, we have performed laboratory experiments to test the effect of relative humidity (RH), grain size (g.s.) and normal stress on rate-and-state frictional properties and stability of fault laboratory analogues corresponding to powders of OPA shaly facies. The sifted host rock powders at different grain size fractions (<63 μm and 63 < g.s. < 125 μm), at room (∼25 per cent) and 100 per cent humidity, were slid in double-direct shear configuration, under different normal stresses (5–70 MPa). We observe that peak friction, μpeak and steady-state friction, μss, depend on water vapour content and applied normal stress. Increasing relative humidity from ∼25 per cent RH (room humidity) to 100 per cent RH causes a decrease of frictional coefficient from 0.41 to 0.35. The analysis of velocity-steps in the light of rate-and-state friction framework shows that the stability parameter (a–b) is always positive (velocity-strengthening), and it increases with increasing sliding velocity and humidity. The dependence of (a–b) on slip rate is lost as normal stress increases, for each humidity condition. By monitoring the variations of the layer thickness during the velocity steps, we observe that dilation (Δh) is directly proportional to the sliding velocity, decreases with normal stress and is unaffected by humidity. Microstructural analysis shows that most of the deformation is accommodated within B-shear zones, and the increase of normal stress (σn) promotes the transition from strain localization and grain size reduction to distributed deformation on a well-developed phyllosilicate network. These results suggest that: (1) the progressive loss of velocity dependence of frictional stability parameter (a–b) at σn > 35 MPa is dictated by a transition from localized to distributed deformation and (2) water vapour content does not affect the deformation mechanisms and dilation, whereas it decreases steady-state friction (μss), and enhances fault stability.

58 GEOSCIENCES↗
DOE OSTI2020

Jeankempite, Ca 5 (AsO 4 ) 2 (AsO 3 OH) 2 (H 2 O) 7 , a new arsenate mineral from the Mohawk Mine, Keweenaw County, Michigan, USA

Abstract Jeankempite, Ca 5 (AsO 4 ) 2 (AsO 3 OH) 2 (H 2 O) 7 , is a new mineral species (IMA2018-090) discovered amongst coatings of arsenate minerals on oxidised copper arsenides from the Mohawk No. 2 mine, Mohawk, Keweenaw County, Michigan, USA. The new mineral occurs as lamellar bundles of colourless to white plates up to 1 mm wide and is visually indistinguishable from guérinite, with which it forms intergrowths. Jeankempite is transparent to translucent with a waxy lustre and white streak, is non-fluorescent under longwave and shortwave ultraviolet illumination, has a Mohs hardness of ~1.5 and brittle tenacity with uneven fracture. Crystals are flattened on {01 $\bar{1}$ } and exhibit perfect cleavage on {01 $\bar{1}$ }. Optically, jeankempite is biaxial (+), α = 1.601(2), β = 1.607(2), γ = 1.619(2) (white light); 2V meas. = 72(2)° and 2V calc. = 71.0°. The empirical formula is (Ca 4.97 Na 0.013 Mg 0.017 )(As 3.99 S 0.01 ) 4 O 23 H 16 , based on 23 O and 16 H atoms per formula unit. Thermogravimetric analysis indicates that jeankempite undergoes four weight losses totalling 16.82%, close to the expected loss of 16.30%, corresponding to eight H 2 O. Jeankempite is triclinic, P $\bar{1}$ , a = 6.710(6), b = 14.901(14), c = 15.940(15) Å, α = 73.583(12)°, β = 81.984(12)°, γ = 82.754(12)°, V = 1507(2) Å 3 and Z = 3. The final structure was refined to R 1 = 0.0591 for 2781 reflections with I obs > 3σ I . The crystal structure of jeankempite is built from a network of edge- and vertex-sharing CaO 6 , CaO 7 and AsO 4 polyhedra, and we hypothesise that the new mineral has formed due to a topotactic reaction brought on by dehydration of preexisting guérinite.

Mineralogy↗
DOE OSTI2020

Multiprincipal Component P2-Na 0.6 (Ti 0.2 Mn 0.2 Co 0.2 Ni 0.2 Ru 0.2 )O 2 as a High-Rate Cathode for Sodium-Ion Batteries

Mixing transition metal cations in nearly equiatomic proportions in layered oxide cathode materials is a new strategy for improving the performances of Na-ion batteries. The mixing of cations not only offers entropic stabilization of the crystal structure but also benefits the diffusion of Na ions with tuned diffusion activation energy barriers. In light of this strategy, a high-rate Na 0.6 (Ti 0.2 Mn 0.2 Co 0.2 Ni 0.2 Ru 0.2 )O 2 cathode was designed, synthesized, and investigated, combining graph-based deep learning calculations and complementary experimental characterizations. This new cathode material delivers high discharge capacities of 164 mA g –1 at 0.1 C and 68 mAh g –1 at a very high rate of 86 C, demonstrating an outstanding high rate capability. Ex situ and operando synchrotron X-ray diffraction were used to reveal the detailed structural evolution of the cathode upon cycling. Using the climbing-image nudged elastic-band calculation and Ab initio molecular dynamics simulations, we show that the optimal transition metal composition enables a percolating network of low barrier pathways for fast, macroscopic Na diffusion, resulting in the observed high rate performance.

25 ENERGY STORAGE↗
DOE OSTI2026

Exploring composition mixing in kilonova ejecta with ray-by-ray simulations

Binary neutron star merger (BNSM) ejecta are considered a primary repository of r-process nucleosynthesis and a source of the observed heavy-element abundances. We implement composition mixing into ray-by-ray radiation-hydrodynamic simulations of BNSM ejecta, coupled with an online nuclear network (NN). We model mixing via a gradient-based mixing approximation that evolves simultaneously with the hydrodynamics. Here, we find that mixing occurs in regions where the electron fraction changes rapidly. While mixing smooths composition gradients in transition regions, it has a negligible impact on the heavy-element yields. This is because the primary r-process site (the equatorial ejecta) is initially homogeneous in free neutrons, leaving no strong gradients for mixing to act upon. In each angular ray, the abundances of the most produced elements are robust under mixing, while the less abundant ones are more affected. The total global abundances change only slightly from mixing, since each angular ray contributes its most abundant elements. Furthermore, the predicted kilonova light curves show only minor reddening, with differences below the detectability of state-of-the-art telescopes. In general, we do not observe significant effects from mixing in the time span of the r-process. Consequently, mixing only leads to minor variations in abundances and light curves in ray-by-ray simulations.

Explosive burning↗
DOE OSTI2023

Student Travel Support for the Inaugural Gordon Research Seminar on Multiphoton Processes (Final Technical Report)

This project provided financial support for early-career participants of the 2022 Gordon Research Seminar (GRS) on Multiphoton Processes, which was held on June 11 & 12, 2022 in Smithfield, Rhode Island, in conjunction with the Gordon Research Conference (GRC) on the same topic, held on June 12-17, 2022 in the same location. The GRC on Multiphoton Processes is an established conference series in the field of Atomic, Molecular and Optical (AMO) Physics with intense lasers. It regularly attracts around one hundred fifty researchers from around the world to present and discuss their forefront research featuring light-matter interaction in a variety of systems, ranging from atoms and molecules to nanosystems. In order to increase the attendance of early-career researchers at the GRC, in particular graduate students, post-docs, and other scientists with comparable levels of experience and education, the general assembly of the GRC on Multiphoton Processes decided during their last session in 2018 to organize a Gordon Research Seminar in conjunction with the next conference and organized and attended by early-career researchers. The GRS's primary intent is to provide a forum to graduate students and post-docs working in the field of intense and ultrafast AMO physics to present and exchange new data and cutting-edge ideas and to network with their peers at other research institutions around the U.S. and the world.

74 ATOMIC AND MOLECULAR PHYSICS↗
NASA NTRS2016

James Webb Space Telescope Core 2 Test - Cryogenic Thermal Balance Test of the Observatorys Core Area Thermal Control Hardware

The James Webb Space Telescope (JWST), successor to the Hubble Space Telescope, will be the largest astronomical telescope ever sent into space. To observe the very first light of the early universe, JWST requires a large deployed 6.5-meter primary mirror cryogenically cooled to less than 50 Kelvin. Three scientific instruments are further cooled via a large radiator system to less than 40 Kelvin. A fourth scientific instrument is cooled to less than 7 Kelvin using a combination pulse-tube Joule-Thomson mechanical cooler. Passive cryogenic cooling enables the large scale of the telescope which must be highly folded for launch on an Ariane 5 launch vehicle and deployed once on orbit during its journey to the second Earth-Sun Lagrange point. Passive cooling of the observatory is enabled by the deployment of a large tennis court sized five layer Sunshield combined with the use of a network of high efficiency radiators. A high purity aluminum heat strap system connects the three instrument's detector systems to the radiator systems to dissipate less than a single watt of parasitic and instrument dissipated heat. JWST's large scale features, while enabling passive cooling, also prevent the typical flight configuration fully-deployed thermal balance test that is the keystone of most space missions' thermal verification plans. This paper describes the JWST Core 2 Test, which is a cryogenic thermal balance test of a full size, high fidelity engineering model of the Observatory's 'Core' area thermal control hardware. The 'Core' area is the key mechanical and cryogenic interface area between all Observatory elements. The 'Core' area thermal control hardware allows for temperature transition of 300K to approximately 50 K by attenuating heat from the room temperature IEC (instrument electronics) and the Spacecraft Bus. Since the flight hardware is not available for test, the Core 2 test uses high fidelity and flight-like reproductions.

JWST Thermal Core 2 Test↗
DOE OSTI2022

All‐Printed Ultrahigh‐Responsivity MoS 2 Nanosheet Photodetectors Enabled by Megasonic Exfoliation

Abstract Printed 2D materials, derived from solution‐processed inks, offer scalable and cost‐effective routes to mechanically flexible optoelectronics. With micrometer‐scale control and broad processing latitude, aerosol‐jet printing (AJP) is of particular interest for all‐printed circuits and systems. Here, AJP is utilized to achieve ultrahigh‐responsivity photodetectors consisting of well‐aligned, percolating networks of semiconducting MoS 2 nanosheets and graphene electrodes on flexible polyimide substrates. Ultrathin (≈1.2 nm thick) and high‐aspect‐ratio (≈1 μm lateral size) MoS 2 nanosheets are obtained by electrochemical intercalation followed by megasonic atomization during AJP, which not only aerosolizes the inks but also further exfoliates the nanosheets. The incorporation of the high‐boiling‐point solvent terpineol into the MoS 2 ink is critical for achieving a highly aligned and flat thin‐film morphology following AJP as confirmed by grazing‐incidence wide‐angle X‐ray scattering and atomic force microscopy. Following AJP, curing is achieved with photonic annealing, which yields quasi‐ohmic contacts and photoactive channels with responsivities exceeding 10 3 A W −1 that outperform previously reported all‐printed visible‐light photodetectors by over three orders of magnitude. Megasonic exfoliation coupled with properly designed AJP ink formulations enables the superlative optoelectronic properties of ultrathin MoS 2 nanosheets to be preserved and exploited for the scalable additive manufacturing of mechanically flexible optoelectronics.

2D materials↗
DOE OSTI2024

Information-incorporated gene network construction with FDR control

Abstract Motivation Large-scale gene expression studies allow gene network construction to uncover associations among genes. To study direct associations among genes, partial correlation-based networks are preferred over marginal correlations. However, FDR control for partial correlation-based network construction is not well-studied. In addition, currently available partial correlation-based methods cannot take existing biological knowledge to help network construction while controlling FDR. Results In this paper, we propose a method called Partial Correlation Graph with Information Incorporation (PCGII). PCGII estimates partial correlations between each pair of genes by regularized node-wise regression that can incorporate prior knowledge while controlling the effects of all other genes. It handles high-dimensional data where the number of genes can be much larger than the sample size and controls FDR at the same time. We compare PCGII with several existing approaches through extensive simulation studies and demonstrate that PCGII has better FDR control and higher power. We apply PCGII to a plant gene expression dataset where it recovers confirmed regulatory relationships and a hub node, as well as several direct associations that shed light on potential functional relationships in the system. We also introduce a method to supplement observed data with a pseudogene to apply PCGII when no prior information is available, which also allows checking FDR control and power for real data analysis. Availability and implementation R package is freely available for download at https://cran.r-project.org/package=PCGII.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1995

Silicon Micromachining in RF and Photonic Applications

Texas Instruments (TI) has developed membrane and micromirror devices since the late 1970s. An eggcrate space membrane was used as the spatial light modulator in the early years. Discrete micromirrors supported by cantilever beams created a new era for micromirror devices. Torsional micromirror and flexure-beam micromirror devices were promising for mass production because of their stable supports. TI's digital torsional micromirror device is an amplitude modulator (known as the digital micromirror device (DMD) and is in production development, discussed elsewhere. We also use a torsional device for a 4 x 4 fiber-optic crossbar switch in a 2 cm x 2 cm package. The flexure-beam micromirror device is an analog phase modulator and is considered more efficient than amplitude modulators for use in optical processing systems. TI also developed millimeter-sized membranes for integrated optical switches for telecommunication and network applications. Using a member in radio frequency (RF) switch applications is a rapidly growing area because of the micromechanical device performance in microsecond-switching characteristics. Our preliminary membrane RF switch test structure results indicate promising speed and RF switching performance. TI collaborated with MIT for modeling of metal-based micromachining.

Lin, Tsen-Hwang↗
DOE OSTI2025

Mesoscale Modeling of Hydrogels Under Frictional Shear Stress

Hydrogels are three-dimensional networks of hydrophilic polymers often used as a simplified model of hydrated biological materials, from cartilaginous joints to the ocular tear film. However, the lubrication mechanisms of hydrogels remain poorly understood, partly due to their complex polymeric structure, which creates blurred interfaces during sliding that are challenging to study experimentally. In this study, we employ dissipative particle dynamics (DPD) to investigate the frictional behavior of a polymeric hydrogel network sliding against a solid wall in an explicit viscous solvent. This computational approach enables us to model hydrodynamic interactions and mesoscale polymer dynamics, capturing key aspects of hydrogel friction. Our simulations reveal that hydrogel friction is governed by the interplay between polymer relaxation and viscous shear, characterized by the Weissenberg number (Wi). At low Wi, friction coefficient remain nearly constant, dominated by polymer relaxation. However, at higher Wi, friction is dominated by viscous drag within a near-wall solvent layer, leading to a linear increase in friction coefficient with Wi. Furthermore, our results demonstrate an inverse relationship between the friction coefficient and the applied normal load, consistent with experimental observations. This work provides new insights into the fundamental tribological properties of hydrogels, shedding light on the micromechanics of hydrogel friction. Improving our understanding of hydrogel structure and dynamics under friction advances our knowledge of the mechanisms regulating biological lubrication in health and disease.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Role of depth in optical diffractive neural networks

Free-space all-optical diffractive neural networks have emerged as promising systems for neuromorphic scene classification. Understanding the fundamental properties of these systems is important to establish their ultimate performance. Here we consider the case of diffraction by subwavelength apertures and study the behavior of the system as a function of the number of diffractive layers by employing a co-design modeling approach. We show that adding depth allows the system to achieve high classification accuracies with a reduced number of diffractive features compared to a single layer, but that it does not allow the system to surpass the performance of an optimized single layer. The improvement from depth is found to be limited to the first few layers. These properties originate from the constraints imposed by the physics of light, in particular the weakening electric field with distance from the aperture.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Context matters: Natural tree mortality can lead to neighbor growth release or suppression

Where competition suppresses tree growth, mortality of adjacent trees can release the surviving individuals, leading to a growth increase. However, primary forests are complicated systems, where trees interact in both competitive and facilitative ways mediated by their size, species, and the broad ecological context in which they grow. Thus, the magnitude and even direction of growth responses to the mortality of nearby trees may vary, which has implications for our understanding of community- and ecosystem-level dynamics following mortality events. Unfortunately, although many studies focus on the impacts of light availability and general crowding on tree growth, we know relatively little about the effects of naturally occurring mortality events on the growth of neighboring trees. To address this issue, we used 40 years of data from 15 permanent forest-monitoring plots in Mt Rainier old-growth forests, comparing observed to expected radial growth of individual trees following the death of their nearest neighbor. Although we found evidence of a general growth-release response, this was not universal among all trees, with small trees in particular exhibiting growth suppression (rather than release) following neighboring tree mortality. In addition to small size, growth-suppression was more likely if the dead neighbor was the same species, consistent with facilitative effects as mediated through belowground networks. At the stand level, the average growth release after nearest neighbor mortality was greatest in low-density stands with large trees, with elevation and community composition also playing a role. Decades more monitoring could reveal how long growth release (or suppression) is sustained by individual trees following neighboring mortality events, as well as potential response lags and the role of species identity in determining whether interactions with neighbors are competitive or facilitative. Nonetheless, our results suggest that although mature trees have competitive effects on their larger neighbors, they also have an important role in supporting the ingrowth of small trees. More broadly, we demonstrate that the nature of interactions between individual neighboring trees is highly context dependent.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1999

A LIS Validation Study at the KSC-ER using LDAR and Field Mill Data

The chance of having the TRMM satellite pass over east central Florida when there is lightning over the NASA Kennedy Space Center (KSC) and USAF Eastern Range (ER) is small; however, such a condition did occur on September 21, 1998 (Day 264). Starting at about 20:40 GMT, the Lightning Imaging Sensor (LIS) reported 5 flashes during a 90 second interval that the KSC-ER was within the sensor field of view. Ground-based instrumentation, the Lightning Detection and Ranging (LDAR) system and a network of electric field mills (FM), detected 6 flashes in the same interval. In this paper, we will compare the times and locations of the optical pulses that were detected by LIS with the times and locations of RF sources (LDAR) and the charges that were deposited by the flash (FM network). We will show that LIS responded to all flashes that the LDAR and FM network detected; however, two discharges that were separated by less than 1 second in time and by about 10 km in space were grouped as one flash by the LIS data processing algorithm. In spite of the fact that all flashes occurred near the edge of the LIS field of view, the locations of the LIS events were consistent with both the LDAR and FM locations (the latter are usually within 1-2 kilometers of each other and often are co-located). Two of the 5 flashes reported by LIS were shifted north by about 8 km from the corresponding LDAR and FM locations. The LIS flash times tended to be after the first LDAR pulse was detected and before the last, and the integrated light signal (per LIS event) was surprisingly constant over the 5 flashes that were detected by LIS. In the future, we plan to study more correlated events and will try to determine whether and how the LIS light signal is related to the charge transfer in the flash and/or the number and spatial extent of RF sources.

Koshak, William J.↗
DOE OSTI2020

A stable and highly selective metalloporphyrin based framework for the catalytic oxidation of cyclohexene

A new metalloporphyrin framework of molybdenum Mo 2 O 4 (C 48 H 28 N 4 O 8 )·(CH 3 ) 2 NH·5H 2 O·2DMF (Mo 2 TCPP) was synthesized from tetrakis(4-carboxyphenyl)porphyrin (H 4 TCPP) and sodium molybdate dihydrate by a hydrothermal method. Mo 2 TCPP is a 3D network with two sub-units, in which both TCPP ligands and each Mo 2 dimer act as four connection nodes. The crystal structure was determined by single crystal analysis and further characterized by FTIR, SEM, EDX, PXRD, XPS and TGA. Here cumene hydrogen peroxide and hydrogen peroxide were used as oxidants to study the catalytic activity of new metalloporphyrins in the oxidation of cyclohexene at different temperatures. The conversion rate of cyclohexene and the selectivity of epoxycyclohexane were both higher than 99%, which was better than the previously published research results. The stability of the catalyst before and after the reaction was further tested for 10 runs without obvious degradation. The catalyst was stable in different solutions such as acidic, water and alkaline. These results shed light on the future development of new catalytic materials based on metalloporphyrin.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Liquid-phase mega-electron-volt ultrafast electron diffraction

The conversion of light into usable chemical and mechanical energy is pivotal to several biological and chemical processes, many of which occur in solution. To understand the structure–function relationships mediating these processes, a technique with high spatial and temporal resolutions is required. Here, we report on the design and commissioning of a liquid-phase mega-electron-volt (MeV) ultrafast electron diffraction instrument for the study of structural dynamics in solution. Limitations posed by the shallow penetration depth of electrons and the resulting information loss due to multiple scattering and the technical challenge of delivering liquids to vacuum were overcome through the use of MeV electrons and a gas-accelerated thin liquid sheet jet. To demonstrate the capabilities of this instrument, the structure of water and its network were resolved up to the 3rd hydration shell with a spatial resolution of 0.6 Å; preliminary time-resolved experiments demonstrated a temporal resolution of 200 fs.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Factorized visual representations in the primate visual system and deep neural networks

Object classification has been proposed as a principal objective of the primate ventral visual stream and has been used as an optimization target for deep neural network models (DNNs) of the visual system. However, visual brain areas represent many different types of information, and optimizing for classification of object identity alone does not constrain how other information may be encoded in visual representations. Information about different scene parameters may be discarded altogether (‘invariance’), represented in non-interfering subspaces of population activity (‘factorization’) or encoded in an entangled fashion. In this work, we provide evidence that factorization is a normative principle of biological visual representations. In the monkey ventral visual hierarchy, we found that factorization of object pose and background information from object identity increased in higher-level regions and strongly contributed to improving object identity decoding performance. We then conducted a large-scale analysis of factorization of individual scene parameters – lighting, background, camera viewpoint, and object pose – in a diverse library of DNN models of the visual system. Models which best matched neural, fMRI, and behavioral data from both monkeys and humans across 12 datasets tended to be those which factorized scene parameters most strongly. Notably, invariance to these parameters was not as consistently associated with matches to neural and behavioral data, suggesting that maintaining non-class information in factorized activity subspaces is often preferred to dropping it altogether. Thus, we propose that factorization of visual scene information is a widely used strategy in brains and DNN models thereof.

59 BASIC BIOLOGICAL SCIENCES↗
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↗