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At least 127 records · Page 7

Microbial Models for Simulating Soil Carbon Dynamics: A Review

Abstract Soils store the largest amount of carbon (C) in the biosphere, and the C pool in soil is critical to the global C balance. Numerous microbial models have been developed over the last few decades to represent microbial processes that regulate the responses of soil organic carbon (SOC) to climate change. However, the representation of microbial processes varies, and how microbial processes are incorporated into SOC models has not been well explored. Here, we reviewed 71 microbial models to characterize the microbial processes incorporated into SOC models and analyzed variations in mechanistic complexity. We revealed that (a) four processes (microbial‐mediated decomposition, mineral interaction, microbial necromass recycling, and active and dormant microbial dynamics) are commonly incorporated in microbial models, (b) ∼48% of models simulate only one microbial process (i.e., microbial‐mediated decomposition) and 35% of models simulate two microbial processes: for example, microbial‐mediated decomposition and mineral interaction, (c) more than 80% microbial models use nonlinear equations, such as forward Michaelis‐Menten kinetics, to represent SOC decomposition, (d) the concept of persistence of SOC due to its intrinsic properties has been replaced by organo‐mineral interaction (∼39% of microbial models) that protects SOC from decomposition, and (e) various temperature and moisture modifiers and pH effects have been used to explain the environmental effect on microbial processes. In the future, to realistically incorporate microbial processes into Earth System Models, it is imperative to identify experimental evidence on rate limitation processes and firmly ground model structure on the field and laboratory data.

Environmental Sciences & Ecology↗

MOFLUX Intensified Soil Moisture Extremes Decrease Soil Organic Carbon Decomposition: Modeling Archive

This Modeling Archive is in support the publication “Intensified Soil Moisture Extremes Decrease Soil Organic Carbon Decomposition: A Mechanistic Modeling Analysis” (Liang et al., 2021). Here we provide model code, inputs, outputs and evaluation datasets for the Microbial ENzyme Decomposition (MEND) model for the Missouri Ozarks AmeriFlux eddy covariance measurement site (MOFLUX) near Ashland, Missouri USA. The MEND model was developed with explicit representation of microbial and enzyme pools to mechanistically simulate the role of microbial organisms and extracellular enzymes in soil organic carbon (SOC) decomposition. Long-term SOC dynamics under intensified moisture extremes are studied using the MEND model that is parameterized with 11 years of measurements from the MOFLUX forest. The model explicitly represents microbial dormancy and resuscitation, different types of SOC-degrading enzymes, and how they vary with changes in soil moisture (Wang et al. 2015, 2019). A combination of two levels of frequency and severity of soil moisture, as well as a control with normal interannual variability, are used to simulate a range of moisture scenarios over 100 years. The code of Microbial-ENzyme Decomposition (MEND) as well as the input and output data are included in the archive. A user’s manual (MEND_Readme.pdf) is included with instructions for compiling and running the model to simulate soil organic carbon decomposition under various moisture scenarios. This dataset contains the modelling archive contained within a compressed (*.zip) file, a file-level metadata file in comma separate (*.csv) format, and two instructional files in PDF (*.pdf) format.

54 ENVIRONMENTAL SCIENCES↗

Quantum Computer-Aided Design: Digital Quantum Simulation of Quantum Processors

With the increasing size of quantum processors, submodules that constitute the processor hardware will become too large to accurately simulate on a classical computer. Therefore, one would soon have to fabricate and test each new design primitive and parameter choice in time-consuming coordination between design, fabrication, and experimental validation. Here we show how one can design and test the performance of next-generation quantum hardware—by using existing quantum computers. Focusing on superconducting transmon processors as a prominent hardware platform, we compute the static and dynamic properties of individual and coupled transmons. We show how the energy spectra of transmons can be obtained by variational hybrid quantum-classical algorithms that are well suited for near-term noisy quantum computers. In addition, single- and two-qubit gate simulations are demonstrated via Suzuki-Trotter decomposition. Our methods pave a promising way towards designing candidate quantum processors when the demands of calculating submodule properties exceed the capabilities of classical computing resources.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Ignition delay time and speciation of dibutyl ether at high pressures

Dibutyl ether (DBE) is a promising biofuel due to its high cetane number (~ 100) and high volumetric energy density (31.6 MJ/L). It could either be used directly in compression ignition engines or blended with other conventional or renewable fuels. Oxidation and pyrolysis kinetics of DBE are not well known, particularly at high pressures. In this work, we have experimentally investigated the chemical kinetics of DBE in three domains: (a) ignition delay time measurements in a rapid compression machine over T = 550–650 K, P = 10, 20, 40 bar, φ = 0.5, 1; (b) ignition delay time measurements in a shock tube over T = 900–1300 K, P = 20, 40 bar, φ = 0.5, 1; (c) laser-based carbon monoxide speciation measurements in a shock tube during DBE pyrolysis and oxidation over T = 1100–1400 K, P = 20 bar. Pressure time-histories measured in RCM experiments exhibited unique 3-stage and 4-stage ignition behavior predominantly at fuel-lean conditions. Experimental data were compared with the predictions of two recent chemical kinetic models of DBE. Sensitivity analyses were carried out to identify key reactions which may have caused the discrepancy between experiments and simulations. We found that the rate of decomposition of DBE may need to be revisited to improve the oxidative and pyrolytic predictions of DBE kinetic model.

09 BIOMASS FUELS↗

Tailoring Interfaces in Solid-State Batteries Using Interfacial Thermochemistry and Band Alignment

Solid-state lithium ion batteries have enhanced thermal stability compared to batteries using liquid electrolytes. Although their practical implementation is limited by undesired side reactions between the electrode and electrolyte, different modification strategies have been proposed to stabilize these reactive interfaces. These approaches have been primarily based upon bulk materials properties, however, which may not necessarily be representative of the chemistry at the solid/solid interface. In this work, first principles calculations and X-ray scattering experiments are used to elucidate molecular-level reactivity and develop design principles for tailored interfaces based on surface and interfacial properties. Because of its well-known instability, the interface between the Li metal anode and the lithium lanthanum titanate (LLTO) solid electrolyte is applied as a model system. Density functional theory calculations are used to describe bulk, surface, and interfacial thermochemistry of the Li/LLTO system, and interfacial reconstruction is probed using ab initio molecular dynamics. These simulations of the Li/LLTO interface demonstrate facile decomposition concomitant with reduction of Ti 4+ ions. Based on further insights from computational analysis of the surface band edge positions, La 2 O 3 is proposed as an interlayer coating and is shown to provide an energetic barrier for interfacial charge transfer and decomposition reactions from X-ray reflectivity measurements and theoretical calculations. The findings in this work suggest that design strategies based on surface and interfacial properties can be used to kinetically stabilize electrode/electrolyte interfaces in solid-state batteries.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Quantifying the Decomposition Kinetics of Linear C 2 –C 4 Perfluoroalkanes

The pyrolysis of C 2 –C 4 linear perfluoroalkanes was investigated using laser schlieren densitometry (LS) in a diaphragmless shock tube. Mixtures of 1, 2, and 4% perfluoroethane (PFE), perfluoropropane (PFP), and perfluorobutane (PFB) in excess krypton were shock-heated to 1400–2500 K at pressures of 60, 120, and 240 Torr. The initiation step for all perfluoroalkanes involved carbon–carbon bond fission. The rate constants for unimolecular decomposition were computed using microcanonical rate theory, and these rate constants were combined into a detailed chemical kinetic mechanism. For PFE and PFP, there was one dissociation channel, while PFB dissociated via two competing bond-fission reactions. The perfluoroalkyl radicals subsequently recombined or underwent further unimolecular decomposition. In conclusion, the kinetic model accurately simulated the density gradient profiles of all perfluoroalkanes.

Guzman, Eduardo H. [Brown Univ., Providence, RI (U↗

Implications of Shear and Thermal Stratification on Wind Turbine Tip-Vortex Stability

The interaction between wind turbines in a wind farm through their wakes is a phenomenon that has been studied for decades and is still relevant today. Turbines clustered together in arrays will often operate in the wake of other upstream turbines which may lead to significant power losses and fatigue loads. For modern large-scale wind turbines, the mean shear velocity profile and thermal stratification are major components of the atmospheric boundary layer so it is important to understand their impact on near-wake development. Additionally, veer is present due to the rotation of the Earth. The impact of shear, thermal stratification and veer on the stable wake length of turbines with a dynamic control strategy is studied numerically in this work using a suite of highly resolved large-eddy simulations. Instantaneous flow fields are extracted from the simulations and used to conduct proper orthogonal decomposition (POD) and compute the mean kinetic energy fluxes by different POD modes to better understand the tip-vortex instability mechanisms. Our findings show that the dynamic pitch control scheme is able to shorten the stable wake length to about 1.5R in uniform flow. Shear can significantly affect the break up of wind turbine tip-vortices as well as the shape and stable length of the wake, whereas thermal stratification seems to only have limited contribution to the spatial development of the near-wake field. Veer causes the wake boundary to skew but has a limited impact on the wake length.

length thermal stratification↗

Developments in SRW Code and Sirepo Framework Supporting Simulation of Time-Dependent Coherent X-ray Scattering Experiments

Physical optics simulations for beamlines and experiments are essential for the effective use of synchrotron light source facilities such as NSLS-II at BNL. The SRW software package supports such source-to-detector simulations for coherent X-ray scattering and imaging experiments through its Python interface and Sirepo browser-based graphical user interface. This allows one to define custom sample models, assess the feasibility of an experiment, and estimate most appropriate beamline settings before using valuable beamtime. We discuss the recent use of general-purpose GPU resources and coherent mode decomposition algorithms in SRW to accelerate physical optics simulations with partially coherent X-rays. To illustrate these new capabilities, we describe simulations of typical time series of partially coherent scattering images used in X-ray Photon Correlation Spectroscopy (XPCS) experiments; aiming to characterize the nanoscale dynamics of a disordered sample, representing a solution of nanoparticles undergoing Brownian diffusion.

36 MATERIALS SCIENCE↗

Simulating measurable ecosystem carbon and nitrogen dynamics with the mechanistically defined MEMS 2.0 model

Abstract. For decades, predominant soil biogeochemical models have used conceptual soil organic matter (SOM) pools and only simulated them to a shallow depth in soil. Efforts to overcome these limitations have prompted the development of the new generation SOM models, including MEMS 1.0, which represents measurable biophysical SOM fractions, over the entire root zone, and embodies recent understanding of the processes that govern SOM dynamics. Here we present the result of continued development of the MEMS model, version 2.0. MEMS 2.0 is a full ecosystem model with modules simulating plant growth with above- and belowground inputs, soil water and temperature by layer, decomposition of plant inputs and SOM, and mineralization and immobilization of nitrogen (N). The model simulates two commonly measured SOM pools – particulate and mineral-associated organic matter (POM and MAOM, respectively). We present results of calibration and validation of the model with several grassland sites in the US. MEMS 2.0 generally captured the soil carbon (C) stocks (R2 of 0.89 and 0.6 for calibration and validation, respectively) and their distributions between POM and MAOM throughout the entire soil profile. The simulated soil N matches measurements but with lower accuracy (R2 of 0.73 and 0.31 for calibration and validation of total N in SOM, respectively) than for soil C. Simulated soil water and temperature were compared with measurements, and the accuracy is comparable to the other commonly used models. The seasonal variation in gross primary production (GPP; R2 = 0.83), ecosystem respiration (ER; R2 = 0.89), net ecosystem exchange (NEE; R2 = 0.67), and evapotranspiration (ET; R2 = 0.71) was well captured by the model. We will further develop the model to represent forest and agricultural systems and improve it to incorporate new understanding of SOM decomposition.

54 ENVIRONMENTAL SCIENCES↗

Targeted electrochemical reduction of carcinogenic N -nitrosamines from emission control systems within CO 2 capture plants

N-Nitrosamines are one of the environmentally significant byproducts from aqueous amine-based post-combustion carbon capture systems (CCS) due to their potential risk to human health. Safely mitigating nitrosamines before they are emitted from these CO 2 capture systems is therefore a key concern before widescale deployment of CCS can be used to address worldwide decarbonization goals. Electrochemical decomposition is one viable route to neutralize these harmful compounds. The circulating emission control waterwash system, commonly installed at the end of the flue gas treatment trains to minimize amine solvent emissions, plays an important role to capture N-nitrosamines and control their emission into the environment. The waterwash solution is the last point where these compounds can be properly neutralized before becoming an environmental hazard. In this study, the decomposition mechanisms of N-nitrosamines in a simulated CCS waterwash with residual alkanolamines was investigated using several laboratory-scale electrolyzers utilizing carbon xerogel (CX) electrodes. Hcell experiments revealed that N-nitrosamines were decomposed through a reduction reaction and are converted into their corresponding secondary amines thereby neutralizing their environmental impact. Batch-cell experiments statistically examined the kinetic models of N-nitrosamine removal by a combined adsorption and decomposition processes. The cathodic reduction of the N-nitrosamines statistically obeyed the first-order reaction model. Finally, a prototype flow-through reactor using an authentic waterwash was used to successfully target and decompose N-nitrosamines to below the detectable level without degrading the amine solvent compounds allowing them to be return to the CCS and lower the system operating costs. Furthermore, the developed electrolyzer was able to efficiently remove greater than 98% of N-nitrosamines from the waterwash solution without producing any additional environmentally harmful compounds and offers an effective and safe route to mitigate these compounds from CO 2 capture systems.

20 FOSSIL-FUELED POWER PLANTS↗

Data and scripts associated with a manuscript modeling microbial regulation of priming effects

This data package is associated with the publication “Modeling Microbial Regulatory Feedback in Organic Matter Decomposition Identifies Copiotrophic Traits as Key Drivers of Positive Priming” published as a preprint on BioRXiv by Ahamed et al. (2026); https://doi.org/10.1101/2024.08.11.607483. The package contains MATLAB scripts and saved simulation outputs used to implement a cybernetic model of microbial regulation during complex organic matter (OM) decomposition governing priming effects. It includes models of (i) single microbial functional groups (copiotrophic or oligotrophic degraders) and (ii) binary consortia composed of degraders and non-degraders with contrasting or common growth traits. Simulation results were generated using Monte Carlo analyses, with randomized key model parameters across a range of environmental mixing fractions of complex and labile OM. The dataset was created to provide a transparent and reusable computational framework for systematically exploring how microbial growth traits, metabolic regulation, and community composition influence OM decomposition dynamics and priming effects. For details on how to navigate data packages generated by this project, see https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. In addition to a readme, this data package also includes a file-level metadata (FLMD) file that describes each file and a data dictionary (DD) that describes the variable definitions. This package includes: (1) annotated MATLAB code implementing the system of ordinary differential equations and cybernetic control laws; (2) saved output files containing data (e.g., biomass, substrates, enzyme levels, priming metrics); and (3) scripts for processing saved outputs and regenerating figures. Specifically, the data package contains three main MATLAB scripts: runPrimingModel.m, runPlotData.m, and runPlotSuppFigS1.m, along with this readme and supporting documentation. Users should begin with runPrimingModel.m, which contains the annotated code implementing the system of ordinary differential equations and cybernetic control laws. This script runs the Monte Carlo simulations of microbial OM decomposition and allows users to modify microbial trait definitions, adjust parameter distributions, or define new community configurations. Simulation outputs are automatically saved as .mat files in the folder named SavedData, which stores all pre-generated results included in this package. The second script, runPlotData.m, reads files from the SavedData folder and processes them to regenerate the figures presented in the manuscript. The third script, runPlotSuppFigS1.m, specifically generates Figure S1 in the Supplementary Material of the manuscript. The package also includes the aforementioned files in non-proprietary .txt format. If users intend to use them, they should first save the files in their respective .m or .mat formats prior to execution in MATLAB.

Biomass concentration↗

Low rank approximation in simulations of quantum algorithms

Simulating quantum algorithms on classical computers is challenging when the system size, i.e., the number of qubits used in the quantum algorithm, is moderately large. However, some quantum algorithms and the corresponding quantum circuits can be simulated efficiently on a classical computer if the input quantum state is a low rank tensor and all intermediate states of the quantum algorithm can be represented or approximated by low rank tensors. Here, in this paper, we examine the possibility of simulating a few quantum algorithms by using low-rank canonical polyadic (CP) decomposition to represent the input and all intermediate states of these algorithms. Two rank reduction algorithms are used to enable efficient simulation. We show that some of the algorithms preserve the low rank structure of the input state and can thus be efficiently simulated on a classical computer. However, the rank of the intermediate states in other quantum algorithms can increase rapidly, making efficient simulation more difficult. To some extent, such difficulty reflects the advantage or superiority of a quantum computer over a classical computer. As a result, understanding the low rank structure of a quantum algorithm allows us to identify algorithms that can benefit significantly from quantum computers.

97 MATHEMATICS AND COMPUTING↗

X-composer: enabling cross-environments in-situ workflows between HPC and cloud

As large-scale scientific simulations and big data analyses become more popular, it is increasingly more expensive to store huge amounts of raw simulation results to perform post-analysis. To minimize the expensive data I/O, "in-situ" analysis is a promising approach, where data analysis applications analyze the simulation generated data on the fly without storing it first. However, it is challenging to organize, transform, and transport data at scales between two semantically different ecosystems due to the distinct software and hardware difference. To tackle these challenges, we design and implement the X-Composer framework. X-Composer connects cross-ecosystem applications to form an "in-situ" scientific workflow, and provides a unified approach and recipe for supporting such hybrid in-situ workflows on distributed heterogeneous resources. X-Composer reorganizes simulation data as continuous data streams and feeds them seamlessly into the Cloud-based stream processing services to minimize I/O overheads. For evaluation, we use X-Composer to set up and execute a cross-ecosystem workflow, which consists of a parallel Computational Fluid Dynamics simulation running on HPC, and a distributed Dynamic Mode Decomposition analysis application running on Cloud. Our experimental results show that X-Composer can seamlessly couple HPC and Big Data jobs in their own native environments, achieve good scalability, and provide high-fidelity analytics for ongoing simulations in real-time.

Wang, Dali↗

Data-Driven Adaptive Damping Controller for Wind Power Plants with Doubly-Fed Induction Generators

This paper presents an adaptive damping controller for wind power plants in which the turbines are equipped with doubly-fed induction generators. The controller is designed to respond to an input control signal that is triggered according to the system operating conditions. A processing unit continuously estimates the electromechanical modes of oscillation based on real-time streaming data acquired from a phasor measurement unit that is strategically positioned on the grid. The decision to trigger (or not trigger) the control signal is automatic, based on the relative damping of the dominant mode. The modes are estimated using the dynamic mode decomposition algorithm with time-delay embedding. Numerical simulations performed on the two-area system demonstrate that the proposed controller enhances the rotor angle stability for both small-signal and large disturbances, and is adaptive to changing grid conditions.

damping controller↗

Plant roots stimulate the decomposition of complex, but not simple, soil carbon

Roots release carbon into soil and can alleviate energy limitation of microbial organic matter decomposition. We know little about the effects of roots on microbial decomposition of different organic matter substrates, despite the importance for soil carbon stocks and turnover. Through implementing root-microbe interactions, the Carbon, Organisms, Rhizosphere, and Protection in the Soil Environment (CORPSE) model was previously shown to represent dynamics of total soil carbon in temperate forest field experiments. However, the model permits alternative hypotheses concerning microbial-substrate affinity. We investigated how root inputs affect decomposition of soil organic carbon (SOC) with variable decomposability. We simulated SOC stocks in CORPSE and compared microbial degradation of two substrates types with varying root-microbe interactions under two alternative hypotheses that varied in microbial-substrate affinity. We compared our modeled hypotheses to a forest field experiment where we quantified decomposition of isotopically-labeled starch and leaf tissues in soils with manipulated root access to microbes. Here, we tested the hypothesis that decomposition of leaves would be more sensitive to root inputs than decomposition of starch, corresponding to the alternative model hypothesis. In the field study, leaf decomposition increased with root density while starch decomposition was unchanged by root density. Microbial biomass and enzyme activity consistently increased with root inputs in CORPSE and the field study. Our field experiment supported the CORPSE simulations with high microbial-substrate affinity. Roots stimulated microbial growth and enzyme production, which increased degradation of more complex substrates such as leaf tissues. Substrates that were easily decomposed, such as starch, may already be degrading at a maximum rate in the absence of rhizosphere influence because their decomposition rate was unchanged by root inputs. We found that the degree to which roots stimulate microbial decomposition depends on the substrate being decomposed, and that root-microbe interactions influenced SOC stocks in both our model and field experiment. Environmental changes that alter root-microbe interactions could, therefore, alter soil C stocks and biogeochemical cycling, and models of these interactions should incorporate differential influence of rhizosphere inputs on different substrates.

59 BASIC BIOLOGICAL SCIENCES↗

Discriminating Accretion States via Rotational Symmetry in Simulated Polarimetric Images of M87

In 2017 April, the Event Horizon Telescope observed the shadow of the supermassive black hole at the core of the elliptical galaxy Messier 87. While the original image was constructed from measurements of the total intensity, full polarimetric data were also collected, and linear polarimetric images are expected in the near future. We propose a modal image decomposition of the linear polarization field into basis functions with varying azimuthal dependence of the electric vector position angle. We apply this decomposition to images of ray traced general relativistic magnetohydrodynamics simulations of the Messier 87 accretion disk. Furthermore, for simulated images that are physically consistent with previous observations, the magnitude of the coefficient associated with rotational symmetry, β2, is a useful discriminator between accretion states. We find that at 20 μas resolution, $| {\beta }_{2}| $ is greater than 0.2 only for models of disks with horizon-scale magnetic pressures large enough to disrupt steady accretion. We also find that images with a more radially directed electric vector position angle correspond to models with higher black hole spin. Our analysis demonstrates the utility of the proposed decomposition as a diagnostic framework to improve constraints on theoretical models.

79 ASTRONOMY AND ASTROPHYSICS↗

Data-Driven Adaptive Damping Controller for Wind Power Plants with Doubly-Fed Induction Generators: Preprint

This paper presents an adaptive damping controller for wind power plants in which the turbines are equipped with doubly-fed induction generators. The controller is designed to respond to an input control signal that is triggered according to the system operating conditions. A processing unit continuously estimates the electromechanical modes of oscillation based on real-time streaming data acquired from a phasor measurement unit that is strategically positioned on the grid. The decision to trigger (or not trigger) the control signal is automatic, based on the relative damping of the dominant mode. The modes are estimated using the dynamic mode decomposition algorithm with time-delay embedding. Numerical simulations performed on the two-area system demonstrate that the proposed controller enhances the rotor angle stability for both small-signal and large disturbances, and is adaptive to changing grid conditions.

61 RADIATION PROTECTION AND DOSIMETRY↗

Block-Structured Operator Inference for Coupled Multiphysics Model Reduction

This work presents a block-structured formulation of Operator Inference as a way to learn structured reduced-order models for multiphysics systems. The approach specifies the governing equation structure for each physics component and the structure of the coupling terms. Once the multiphysics structure is specified, the reduced-order model is learned from snapshot data following the nonintrusive Operator Inference methodology. In addition to preserving physical system structure, which in turn permits preservation of system properties such as stability and second-order structure, the block-structured approach has the advantages of reducing the overall dimensionality of the learning problem and admitting tailored regularization for each physics component. The numerical advantages of the block-structured formulation over a monolithic Operator Inference formulation are demonstrated for aeroelastic analysis, which couples aerodynamic and structural models. For the benchmark test case of the AGARD 445.6 wing, block-structured Operator Inference provides an average 20% online prediction speedup over monolithic Operator Inference across subsonic and supersonic flow conditions in both the stable and fluttering parameter regimes while preserving the accuracy achieved with monolithic Operator Inference.

42 ENGINEERING↗