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DOE OSTI2025

Contributions of vegetation heterogeneity within tower footprint to CO 2 flux estimations through graph neural network modeling

Net ecosystem exchange of CO 2 (Fc) measured directly by eddy covariance towers is based on various assumptions, including large, flat and homogenous land cover type. In reality, often a tower site is not large enough for flux measurements, and landscapes consist of patches of different land cover types within the flux footprint. In addition, some portions of fluxes are contributed by different cover types when a footprint exceeds the size of the target ecosystem. The contributions of non-dominant patches to Fc are often ignored. Here, in this study, we propose a novel integrated modeling framework that combines random forest (RF) and XGBoost with a residual correction module based on a deep graph convolutional network (DeeperGCN) to simulate Fc for seven flux measurement sites in southwest Michigan. High-resolution remote sensing vegetation indices, soil properties, meteorological variables, and footprint-weighted spatial features were used as model inputs at three spatial resolutions (10 m, 20 m, 30 m), and their importance in predicting Fc with DeeperGCN was assessed. We found that residual correction using DeeperGCN significantly improved prediction accuracy, with the R 2 increasing from 0.9098 to 0.9479 for RF and from 0.9235 to 0.9433 for XGBoost. At site level, the maximum improvement in R 2 reached 0.1617. Paired t-tests confirmed that these improvements were statistically significant (p < 0.05). Among all predictors, leaf area index and incoming shortwave radiation emerged as the dominant drivers of spatial residual variation, followed by precipitation, relative humidity, and selected vegetation indices. The 20 m resolution yielded the best balance between model performance and computational efficiency. In conclusion, our modeling framework effectively captures both spatial heterogeneity and nonlinear interactions, offering a robust solution for spatially explicit flux modeling in structurally diverse ecosystems beyond the study sites.

footprint model↗

DOE OSTI2020

An Eulerian multimaterial framework for simulating high-explosive aquarium tests

Aquarium tests of cylindrical high-explosive charges provide optical data of the detonation front velocity and shape, propagation of the shock wave in the surrounding water, and expansion rates of the detonation products behind the front. Data from aquarium experiments is often used for calibration of reactive burn models based on phenomenological equations of state (EOS) and reaction rate laws. This paper presents a multimaterial numerical modeling framework to solve the 2D axisymmetric reactive Euler equations for high-explosive aquarium tests, in particular for ammonium nitrate - fuel oil (ANFO) explosives. An extension of the Ghost Fluid Method (GFM) is used to handle the dynamic material interfaces for the ANFO explosion products, the charge-confining material (polymethyl methacrylate PMMA), and the surrounding water. This study analyzes the sensitivity of calculations (both computational efficiency and numerical accuracy) to different algorithms for the material interface models including the original GFM versus Riemann solver-based strategies. A novel method for defining the left and right states in the interfacial Riemann problem eliminates the need for sorting or nodal interpolation during the projection along the material interface. Numerical tests indicate that populating the interface node values using the Riemann solution mitigate the overheating error observed in steady-state calculations. Solution convergence and computational efficiency are explored as a function of the spatial and temporal order of the schemes. Results from the computational model with analytical equations of state and fitted reaction rate parameters show very good quantitative agreement with experimentally observed detonation front velocity, reaction products expansion, and shock wave propagation in the surrounding water for a cylindrical ANFO charge encased in PMMA. Finally, the proposed modeling framework, in conjunction with experimental tests, provides a reliable tool to assess equations of state and reaction rate expressions for reactive burn models of confined high explosives.

42 ENGINEERING↗

DOE OSTI2020

Evaluating Energy Efficiency Opportunities from Connected and Automated Vehicle Deployments Coupled with Shared Mobility in California

Connected and Automated Vehicles (CAVs) can be considered to be a disruptive transportation technology, with the potential to significantly improve overall transportation system efficiency; however, CAVs may increase induce vehicle miles traveled (VMT) and bring on greater energy consumption. Further, shared mobility is another disruptive transportation event that is reshaping our travel patterns. The primary goal of this project was to extensively collect data from vehicles and associated infrastructure equipped with CAV technologies from both real-world experiments and simulation studies mainly deployed in California, and develop a comprehensive framework for evaluating energy efficiency opportunities from large-scale (e.g., statewide) introduction of CAVs and a wide deployment of shared mobility systems in a variety of scenarios. To quantify the combined impact of CAV and shared mobility on travel behavior, traffic performance, and energy efficiency, a unique mesoscopic simulation-based model was developed for mobility and energy efficiency evaluation considering these disruptive transportation technologies. As a complement to existing studies on nationwide evaluation of CAVs’ energy impacts, this project was focused on data collection efforts and CAV applications under congested traffic environments that are frequently experienced on a massive scale across the major metropolitan areas in California. Extensive real-world data collection supplemented with simulation studies were conducted to cover a variety of CAV and shared mobility scenarios, particularly on scenarios less-explored in the existing research. Another key component of this project was to consider the interaction between different CAV technologies and shared mobility models, and the compound effect on energy efficiency. A comprehensive modeling suite was developed to quantify the impact of new mobility technologies on travel behavior and traffic performance. The developed modeling framework includes an energy intensity module, mode choice module and activity generation module that are integrated into an agent-based BEAM simulation platform to perform impact analysis based on a variety of scenarios. In addition, the RouteE model has been upgraded to incorporate the impact of CAVs on traffic flow, VMT and energy intensity, using micro-simulation data collected from both freeways and urban arterials. A novel fundamental influencing factor (FIF) mode choice model was developed to link CAV and shared mobility components with travel behaviors, and adapted into the BEAM-centered model framework. A statewide energy inventory was constructed under various CAV technology deployment scenarios by incorporating datasets and models for predicting vehicle market share and vehicle usage, which are tightly associated with the penetration of shared mobility systems. Based applying this modeling suite to a calibrated network in Riverside California, it was found that cooperative automated driving in general will improve mobility, but automated vehicles, even when deployed in a shared autonomous fleet, will likely bring an increase of VMT (up to 36%) due to mode shifts and deadheading. Ride-hailing vehicles typically have better energy efficiency and a higher share of electric vehicles, which helps offset the negative impact from VMT increases when estimating the system-level energy consumption. In general, simulation results show a 6% increase in energy consumption for the scenarios with an increasing shift to ride-hailing modes. The statewide analysis based on the National Household Travel Survey (NHTS) sample data is consistent with the findings from the Riverside network and validate the developed clustering-prediction modeling methodology. The outcomes from this project will help close the knowledge gap on recognizing the potential performance and energy impacts of a broad deployment of CAV and shared mobility technologies across a wide range of roadway infrastructure with varying levels of congestion. Results from this project: 1) will support policymakers in steering CAV development and deployment towards an energy favorable direction; 2) reduce uncertainties in estimating energy saving opportunities from new mobility technologies and services; 3) increase the confidence of CAV technology investors both on the infrastructure side (i.e., transportation agencies) and on the vehicle side (i.e., OEMs); and 4) expedite the deployment of energy-efficient CAV and shared mobility applications.

33 ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2025

Challenges of standard halo models in constraining galaxy properties from cosmic infrared background anisotropies

The halo model, combined with halo occupation distribution (HOD) prescriptions, is widely used to interpret cosmic infrared background (CIB) anisotropies and extract physical information about star-forming galaxies and their connection to large-scale structures. Recent CIB-specific implementations of the halo model have adopted more physical parameterizations. However, the extent to which these models can reliably recover meaningful physical parameters remains uncertain. We assessed whether the current parameterization of CIB halo models is sufficient to recover astrophysical quantities, such as star formation efficiency, η(M h , z), and halo mass at which the peak of star formation efficiency occurs, M max , when fit to mock data. We also assessed whether discrepancies arise from assumptions about galaxy emission (the HOD ingredients) or from more fundamental components in the halo model, such as bias and matter clustering. We fit the M21 CIB HOD model, implemented within the halo model framework, to mock CIB power spectra and star formation rate density (SFRD) data generated from the SIDES-Uchuu simulation, and compared the best-fit parameters to the known simulation inputs. We then repeated the analysis using a simplified version of the simulation (SSU), explicitly designed to match the HOD assumptions. A detailed comparison of model and simulation outputs was carried out to trace the origin of observed discrepancies. While the M21 HOD model provides a good fit to the mock data, it failed to recover the intrinsic parameters accurately, particularly the halo mass at which star formation efficiency peaks. This mismatch persists even when fitting data generated with the same model assumptions. We find strong agreement (within 5%) in the emission-related components (SFRD, emissivity), but observe a scale- and redshift-dependent offset exceeding 20% in the two-halo term of the CIB power spectrum. This likely arises from limitations in the treatment of halo bias and matter clustering within the linear approximation. Additionally, incorporating scatter in the SFR–halo mass relation and the spectral energy distribution (SED) templates significantly affects the shot noise (∼50%), but has only a modest impact (less than 10%) on the clustered component. These results suggest that recovering physical parameters from CIB clustering requires improvements to the cosmological ingredients of the halo model framework, such as adopting scale-dependent halo bias and nonlinear matter power spectra in addition to careful modeling of emission physics.

cosmic background radiation↗

DOE OSTI2025

Summary of Multiphysics Modeling for Sublimation Mass Transfer

This report summarizes the effort to develop a multiphysics modeling framework for sublimation mass transfer processes. The aim of the project was to develop a multiphysics code capable of predicting phase change between solid and gas in a closed container, and the movement of material within such a container when exposed to various exterior environmental conditions. Two modeling frameworks were developed towards this aim: one with a high-fidelity computational fluid dynamics (CFD) structure, and the other as a fast reduced-order model. Ultimately, both attempts were unsuccessful due to instabilities in the code and physical processes for which there is no adequate numerical representation. Both modeling attempts are briefly detailed before providing a brief survey of recent updates in the literature, and a recommendation for future work on this subject.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2023

Resolving dynamic mineral-organic interactions in the rhizosphere by combining in-situ microsensors with plant-soil reactive transport modeling

Associations between minerals and organic matter represent one of the most important carbon storage mechanisms in soils. Plant roots are major sources of soil carbon, and resolving the dynamics and dominance of microbial consumption versus mineral sorption of root-derived carbon is critical to understanding soil carbon storage. Here we integrate in-situ rhizosphere microsensor and plant physiological measurements with a 3-D plant-soil reactive transport model to explore the fate of dissolved organic carbon (DOC) in the rhizosphere, particularly its microbial consumption and interaction with Fe oxide minerals. Over several days, a microdialysis probe sampling pore water at the root-soil interface of growing Vicia faba roots in live soil, revealed clear diel patterns of DOC concentration. Daytime DOC spikes coincided with peaks in leaf-level photosynthesis rates and were accompanied by declining redox potential and dissolved oxygen as well as increasing pH in the rhizosphere. Incorporating microsensor data into our modeling framework showed that the measured rapid loss of DOC after each mid-day spike could not be explained by consumption via aerobic respiration, nor via anaerobic respiration dominated by Fe oxide reduction. Rather, in the model, a large fraction of rhizosphere DOC was rapidly immobilized each day by adsorption to Fe oxides. Further, modeled microbial Fe reduction (fueled by DOC) did not mobilize significant organic carbon from Fe oxides during the day. Instead, the model predicted equilibrium desorption of organic carbon from Fe oxides at night. This new mechanistic modeling framework, which couples aboveground plant physiological measurements with non-destructive high-resolution monitoring of rhizosphere processes, has great potential for exploring the dynamics and balance of the various microbial reactions and mineral interactions controlling carbon transformations and storage in soils.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Dynamics and growth rate implications of ribosomes and mRNAs interaction in E. coli

Understanding how cells grow and adapt under various nutrient conditions is pivotal in the study of biological stoichiometry. Recent studies provide empirical evidence that cells use multiple strategies to maintain an optimal protein production rate under different nutrient conditions. Mathematical models can provide a solid theoretical foundation that can explain experimental observations and generate testable hypotheses to further our understanding of the growth process. In this study, we generalize a modeling framework that centers on the translation process and study its asymptotic behaviors to validate algebraic manipulations involving the steady states. Using experimental results on the growth of E. coli under C-, N-, and P-limited environments, we simulate the expected quantitative measurements to show the feasibility of using the model to explain empirical evidence. Our results support the findings that cells employ multiple strategies to maintain a similar protein production rate across different nutrient limitations. Moreover, we find that the previous study underestimates the significance of certain biological rates, such as the binding rate of ribosomes to mRNA and the transition rate between different ribosomal stages. Furthermore, our simulation shows that the strategies used by cells under C- and P-limitations result in a faster overall growth dynamics than under N-limitation. In conclusion, the general modeling framework provides a valuable platform to study cell growth under different nutrient supply conditions, which also allows straightforward extensions to the coupling of transcription, translation, and energetics to deepen our understanding of the growth process.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Economic analysis of the benefits to petroleum refiners for low carbon boosted spark ignition biofuels

A refinery modeling framework is developed to estimate the benefits of blending high-quality biofuels directly with refinery gasoline components for attaining a premium grade fuel (also termed as Co-Optima Boosted SI gasoline here). Our results change the paradigm of bio-blendstocks (BBs) being competitors to fossil components, by identifying opportunities for refineries to add value to their product slate, from some favorable BB properties. This potential value can be characterized by calculating the breakeven value (BEV), as defined down below. The proposed modeling framework incorporates extensive data from (1) projected product over the next few decades, (2) crude oil and refinery products pricing, and (3) fuel specifications. The complete refinery models serve as a basis for assessing the value of biofuels, assuming profitability remains the same for representative petroleum refinery configurations. Our assessment showed wide range of variation of biofuels BEV from $\$$20-$\$$120/bbl, within the considered blending level and crude prices. Further, the BEV was correlated with the fuel octane ratings such as octane numbers (research, RON and motor octane numbers, MON) and both antiknock index (AKI, average of RON and MON) and sensitivity (S, difference between RON and MON), with a slightly higher correlation with the sensitivity. However, the expected decrease in gasoline demand for the upcoming years could negatively impact biofuels demand and value, in a business-as-usual scenario. Our analysis also showed a more valuable bio-blendstocks incorporation in smaller refineries since they can enhance the capabilities for producing specialty, high-value fuels/products, and introduce high octane-barrels into otherwise constrained blending operations. Additional implications towards refiners include opportunities to rebalance operations, access to high-value fuel markets, and synchronization with broader transportation industry trends. Furthermore, results indicate the value of Co-Optima boosted spark ignition (BSI) efficiency gains can extend to refiners to incentivize decarbonization and diversified feedstock production.

09 BIOMASS FUELS↗

DOE OSTI2024

Data‐driven variational method for discrepancy modeling: Dynamics with small‐strain nonlinear elasticity and viscoelasticity

Abstract The effective inclusion of a priori knowledge when embedding known data in physics‐based models of dynamical systems can ensure that the reconstructed model respects physical principles, while simultaneously improving the accuracy of the solution in the previously unseen regions of state space. This paper presents a physics‐constrained data‐driven discrepancy modeling method that variationally embeds known data in the modeling framework. The hierarchical structure of the method yields fine scale variational equations that facilitate the derivation of residuals which are comprised of the first‐principles theory and sensor‐based data from the dynamical system. The embedding of the sensor data via residual terms leads to discrepancy‐informed closure models that yield a method which is driven not only by boundary and initial conditions, but also by measurements that are taken at only a few observation points in the target system. Specifically, the data‐embedding term serves as residual‐based least‐squares loss function, thus retaining variational consistency. Another important relation arises from the interpretation of the stabilization tensor as a kernel function, thereby incorporating a priori knowledge of the problem and adding computational intelligence to the modeling framework. Numerical test cases show that when known data is taken into account, the data driven variational (DDV) method can correctly predict the system response in the presence of several types of discrepancies. Specifically, the damped solution and correct energy time histories are recovered by including known data in the undamped situation. Morlet wavelet analyses reveal that the surrogate problem with embedded data recovers the fundamental frequency band of the target system. The enhanced stability and accuracy of the DDV method is manifested via reconstructed displacement and velocity fields that yield time histories of strain and kinetic energies which match the target systems. The proposed DDV method also serves as a procedure for restoring eigenvalues and eigenvectors of a deficient dynamical system when known data is taken into account, as shown in the numerical test cases presented here.

Masud, Arif↗

DOE OSTI2023

SALT2 versus SALT3: updated model surfaces and their impacts on type Ia supernova cosmology

ABSTRACT For the past decade, SALT2 has been the most common model used to fit Type Ia supernova (SN Ia) light curves for dark energy analyses. Recently, the SALT3 model was released, which upgraded a number of model features but has not yet been used for measurements of dark energy. Here, we evaluate the impact of switching from SALT2 to SALT3 for a SN cosmology analysis. We train SALT2 and SALT3 on an identical training sample of 1083 well-calibrated Type Ia supernovae, ensuring that any differences found come from the underlying model framework. We publicly release the results of this training (the SALT ‘surfaces’). We then run a cosmology analysis on the public Dark Energy Survey 3-Yr Supernova data sample (DES-SN3YR), and on realistic simulations of those data. We provide the first estimate of the SN + CMB systematic uncertainty arising from the choice of SALT model framework (i.e. SALT2 versus SALT3), Δw = + 0.001 ± 0.005 – a negligible effect at the current level of dark energy analyses. We also find that the updated surfaces are less sensitive to photometric calibration uncertainties than previous SALT2 surfaces, with the average spectral energy density dispersion reduced by a factor of two over optical wavelengths. This offers an opportunity to reduce the contribution of calibration errors to SN cosmology uncertainty budgets.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

A Machine Learning Framework for Modeling Ensemble Properties of Atomically Disordered Materials

Atomic disorder can strongly influence material properties such as charge transport, optical response, and catalytic activity. However, efficiently modeling these disorder effects remains challenging for first-principles methods due to the cost of sampling large configurational spaces and computing complex physical quantities. Recent advances of machine learning techniques, particularly graph neural networks (GNNs), has enabled the efficient and accurate predictions of complex material properties, offering promising tools for studying disordered systems. In this work, we present a general machine-learning-assisted computational framework that integrates equivariant GNNs with Monte Carlo simulations to compute the thermodynamic and ensemble-averaged functional properties of disordered materials. Using the surface-termination-disordered MXene monolayer Ti 3 C 2 T 2–x as a representative system, we find that electrical conductivity exhibits an emergent peak near the order–disorder phase transition temperature due to the interplay between electron scattering and doping. In contrast, optical conductivity remains largely insensitive to local atomic disorder and reflects the global surface chemical composition. These results highlight the role of atomic disorder in affecting material properties and demonstrate the potential of our approach for statistically modeling disorder effects in a wide range of materials such as high-entropy alloys and spin liquids.

MXene↗

DOE OSTI2023

Deformation, dislocation evolution and the non-Schmid effect in body-centered-cubic single- and polycrystal tantalum

A physically-informed continuum crystal plasticity model is presented to elucidate deformation mechanisms, dislocation evolution and the non-Schmid effect in body-centered-cubic (bcc) tantalum widely used as a key structural material for mechanical and thermal extremes. We show the unified structural modeling framework informed by mesoscopic dislocation dynamics simulations is capable of capturing salient features of the large inelastic behavior of tantalum at quasi-static (10 -3 s -1 ) to extreme strain rates (5000 s -1 ) and at low (77 K) to high temperatures (873 K) at both single- and polycrystal levels. Here we also present predictive capabilities of the model for microstructural evolution in the material. To this end, we investigate the effects of dislocation interactions on slip activities, instability and the non-Schmid behavior at the single crystal level. Furthermore, ex situ measurements on crystallographic texture evolution and dislocation density growth are carried out for polycrystal tantalum specimens at increasing strains. Numerical simulation results also support that the modeling framework is capable of capturing the main features of the polycrystal behavior over a wide range of strains, strain rates and temperatures. The theoretical, experimental and numerical results at both single- and polycrystal levels provide critical insight into the underlying physical pictures for micro- and macroscopic responses and their relations in this important class of refractory bcc materials undergoing large inelastic deformations.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Development of a Physics-Based Combustion Model for Engine Knock Prediction

The objective of this project is to improve the prediction of engine knock by developing a new combustion modeling framework. Engine knock is a limiting factor to constrain the increase of fuel efficiency for spark ignition (SI) engines in most passenger cars. Efforts to increase fuel efficiency, increasing the compression ratio or downsizing, lead to the increase in the tendency of the knock occurrence. The knock is an undesired ignition of the end-gas, unburned fuel/air mixture ahead of the spark-ignited premixed flame, resulting in rapid in-cylinder pressure rises and engine damages. The combustion modeling framework developed in this project can consider turbulence-chemistry interactions during end-gas ignition, while using a reasonably detailed chemical mechanism developed for ignition and combustion reactions under engine relevant conditions, and the subtle characteristics of spark-ignited flame propagation. It is developed in the context of large eddy simulation (LES), which can capture stochastic in-cylinder processes. The developed model is incorporated into a commercial software for engine simulation, CONVERGE CFD, as a user defined function, and validated. Engine knock and knock-free experiments as well as direct numerical simulation (DNS) of end-gas ignition in homogeneous turbulence are performed to help model development and provide data sets for model validation. With further validation, the developed model is expected to advance the predictive capability for engine knock simulations and thus contribute to improving the fuel efficiency.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2020

Development of a Physics-Based Combustion Model for Engine Knock Prediction

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2020

Health co-benefits and mitigation costs as per the Paris Agreement under different technological pathways for energy supply

This study assesses the reductions in air pollution emissions and subsequent beneficial health effects from different global mitigation pathways consistent with the 2 °C stabilization objective of the Paris Agreement. We use an integrated modelling framework, demonstrating the need for models with an appropriate level of technology detail for an accurate co-benefit assessment. The framework combines an integrated assessment model (GCAM) with an air quality model (TM5-FASST) to obtain estimates of premature mortality and then assesses their economic cost. The results show that significant co-benefits can be found for a range of technological options, such as introducing a limitation on bioenergy, carbon capture and storage (CCS) or nuclear power. Cumulative premature mortality may be reduced by 17–23% by 2020–2050 compared to the baseline, depending on the scenarios. However, the ratio of health co-benefits to mitigation costs varies substantially, ranging from 1.45 when a bioenergy limitation is set to 2.19 when all technologies are available. As for regional disaggregation, some regions, such as India and China, obtain far greater co-benefits than others.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Impacts of climate change on future hurricane induced rainfall and flooding in a coastal watershed: A case study on Hurricane Harvey

The warming climate is likely to increase hurricane-associated extreme rainfall and lead to sea-level rise (SLR). Thus, how the floods induced by intense hurricanes respond to these potential changes is of great concern. This study investigates the future warmer climate impacts on hurricane-induced extreme rainfall, and—more importantly—the subsequent compound flooding at the watershed scale (from an event-based analysis perspective). To this goal, a modeling framework is designed based on the Distributed Hydrology Soil Vegetation Model (DHSVM), the Two-Dimensional fvand the Regional Community Earth System Model (R-CESM). The framework was applied to Hurricane Harvey (2017) at the Clear Creek watershed (a coastal watershed in the southern Houston) as a case study. The results show that the projected maximum rainfall totals over the watershed would be exacerbated by 17.7 % and 49.7 % in the 2050s and 2090s (respectively) under Representative Concentration Pathway 8.5 (RCP 8.5). This means a 16.1 % increase in Harvey rainfall over the watershed per degree Celsius increase in Mean Surface Temperature over the Gulf of Mexico region (18°~31° N, 77°~98° W). Meanwhile, the increases in maximum inundation extent would be 11.0 % (2050s) and 19.5 % (2090s). Furthermore, considerable increases in maximum inundation depth and duration in regions along the middle and downstream of Clear Creek (and also those around Clear Lake) are expected. The projected SLR will have little effect on the maximum inundation depth and extent if storm surge changes are not taken into account; meanwhile, it will influence the inundation duration at downstream locations. In conclusion, this modeling framework can be also applied at other coastal watersheds to evaluate the projected climate change impacts on the compound flooding induced by extreme climate events.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Modeling Growth Kinetics, Interspecies Cell Fusion, and Metabolism of a Clostridium acetobutylicum / Clostridium ljungdahlii Syntrophic Coculture

ABSTRACT Clostridium acetobutylicum and Clostridium ljungdahlii grown in a syntrophic culture were recently shown to fuse membranes and exchange cytosolic contents, yielding hybrid cells with significant shifts in gene expression and growth phenotypes. Here, we introduce a dynamic genome-scale metabolic modeling framework to explore how cell fusion alters the growth phenotype and panel of metabolites produced by this binary community. Computational results indicate C. ljungdahlii persists in the coculture through proteome exchange during fusing events, which endow C. ljungdahlii cells with expanded substrate utilization, and access to additional reducing equivalents from C. acetobutylicum -evolved H 2 and through acquisition of C. acetobutylicum -native cofactor-reducing enzymes. Simulations predict maximum theoretical ethanol and isopropanol yields that are increased by 0.64 mmol and 0.39 mmol per mmol hexose sugar consumed, respectively, during exponential growth when cell fusion is active. This modeling effort provides a mechanistic explanation for the metabolic outcome of cellular fusion and altered homeostasis achieved in this syntrophic clostridial community. IMPORTANCE Widespread cell fusion and protein exchange between microbial organisms as observed in synthetic C. acetobutylicum / C. ljungdahlii culture is a novel observation that has not been explored in silico . The mechanisms responsible for the observed cell fusion events in this culture are still unknown. In this work, we develop a modeling framework that captures the observed culture composition and metabolic phenotype, use it to offer a mechanistic explanation for how the culture achieves homeostasis, and identify C. ljungdahlii as primary beneficiary of fusion events. The implications for the events described in this study are far reaching, with potential to reshape our understanding of microbial community behavior synthetically and in nature.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Demonstration of a code coupling framework for modeling beam-collimator impacts in the advanced photon source

The high-brightness beams being produced in current and future accelerators present new machine protection concerns with the potential for high-energy-density (HED) conditions ( >100 J/mm 3 ) in beam-intercepting components. Simulating HED conditions in accelerators requires utilizing a suite of physics codes for particle dynamics, particle-matter interactions, and hydrodynamics. This paper describes a method of coupling the codes elegant, fluka, and flash to simulate the effects of a rapid beam loss in the advanced photon source storage ring and the resulting interaction of the beam and collimators. This paper expands previous work [J. Dooling et al., Collimator irradiation studies at the advanced photon source, in Proceedings of the IBIC-2023 (2023), pp. 245–249] by introducing a definition of the evolving geometry of the collimator surface as well as providing methods for simulating the absorption of synchrotron radiation and tracking shower particles produced during beam strikes. We demonstrate this framework by simulating machine conditions of the APS ring before and after its recent upgrade. Simulation results are compared with observed damage to collimators and test samples taken from the APS ring.

Accelerator/storage ring control systems↗