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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↗

Soil enzymes as indicators of soil function: A step toward greater realism in microbial ecological modeling

Soil carbon (C) and nitrogen (N) cycles and their complex responses to environmental changes have received increasing attention. However, large uncertainties in model predictions remain, partially due to the lack of explicit representation and parameterization of microbial processes. One great challenge is to effectively integrate rich microbial functional traits into ecosystem modeling for better predictions. Here, using soil enzymes as indicators of soil function, we developed a competitive dynamic enzyme allocation scheme and detailed enzyme-mediated soil inorganic N processes in the Microbial-ENzyme Decomposition (MEND) model. We conducted a rigorous calibration and validation of MEND with diverse soil C-N fluxes, microbial C:N ratios, and functional gene abundances from a 12-year CO 2 × N grassland experiment (BioCON) in Minnesota, USA. In addition to accurately simulating soil CO 2 fluxes and multiple N variables, the model correctly predicted microbial C:N ratios and their negative response to enriched N supply. Model validation further showed that, compared to the changes in simulated enzyme concentrations and decomposition rates, the changes in simulated activities of eight C-N-associated enzymes were better explained by the measured gene abundances in responses to elevated atmospheric CO 2 concentration. In conclusion, our results demonstrated that using enzymes as indicators of soil function and validating model predictions with functional gene abundances in ecosystem modeling can provide a basis for testing hypotheses about microbially mediated biogeochemical processes in response to environmental changes. Further development and applications of the modeling framework presented here will enable microbial ecologists to address ecosystem-level questions beyond empirical observations, toward more predictive understanding, an ultimate goal of microbial ecology.

59 BASIC BIOLOGICAL SCIENCES↗

Multi-year incubation experiments boost confidence in model projections of long-term soil carbon dynamics

Abstract Global soil organic carbon (SOC) stocks may decline with a warmer climate. However, model projections of changes in SOC due to climate warming depend on microbially-driven processes that are usually parameterized based on laboratory incubations. To assess how lab-scale incubation datasets inform model projections over decades, we optimized five microbially-relevant parameters in the Microbial-ENzyme Decomposition (MEND) model using 16 short-term glucose (6-day), 16 short-term cellulose (30-day) and 16 long-term cellulose (729-day) incubation datasets with soils from forests and grasslands across contrasting soil types. Our analysis identified consistently higher parameter estimates given the short-term versus long-term datasets. Implementing the short-term and long-term parameters, respectively, resulted in SOC loss (–8.2 ± 5.1% or –3.9 ± 2.8%), and minor SOC gain (1.8 ± 1.0%) in response to 5 °C warming, while only the latter is consistent with a meta-analysis of 149 field warming observations (1.6 ± 4.0%). Comparing multiple subsets of cellulose incubations (i.e., 6, 30, 90, 180, 360, 480 and 729-day) revealed comparable projections to the observed long-term SOC changes under warming only on 480- and 729-day. Integrating multi-year datasets of soil incubations (e.g., > 1.5 years) with microbial models can thus achieve more reasonable parameterization of key microbial processes and subsequently boost the accuracy and confidence of long-term SOC projections.

54 ENVIRONMENTAL SCIENCES↗

Data for Zheng et al. (2025), "AquaMEND: Reconciling multiple impacts of salinization on soil carbon biogeochemistry"

Soil salinization, exacerbated by climate change, poses a global threat to coastal ecosystems and soil function. Salinity affects soil carbon cycling by directly impacting microbial activity and indirectly altering soil physicochemical properties, but current models inadequately represent these complexities. This dataset contains the observational and modeling data from Zheng et al. (2025), which described a process-based modeling framework that couples soil solution chemistry with microbial carbon cycling reactions to study the impacts of soil salinization. This conceptual model is implemented numerically into the open-source geochemical program PHREEQC 3.0 (Parkhurst and Appelo, 2013). This dataset consists of: - Figure2_AquaMEND_salinity_buffer: Contains model simulation outputs to assess the impact of three different cation exchange and surface complexation processes on salinity buffering (Fig. 2 from Zheng et al. 2025). - Figure3_Salinity_function: Contains salinity function fitting for literature data (Fig. 3 from Zheng et al. 2025). - Figure4_AquaMEND_microbial_mechanisms: Contains model simulation outputs for testing various microbial process-based hypotheses related to soil salinization, including microbial mortality, carbon use efficiency (CUE), extracellular enzyme activity, and other microbial mechanisms (Fig. 4 from Zheng et al. 2025). - Figure5_AquaMEND_Redox: Contains on model simulation outputs to evaluate shifts among key redox processes, such as aerobic respiration, sulfate reduction, and methanogenesis (Fig.5 from Zheng et al. 2025). - Figure6_AquaMEND_sorption: Contains on model simulation outputs for investigating the effects of salinity on dissolved organic matter (DOM) sorption and desorption processes (Fig. 6 from Zheng et al. 2025). - Figure7_AquaMEND_process_couple: Contains on model simulation outputs for exploring coupled biotic-abiotic processes and their interactions (Fig. 7 from Zheng et al. 2025). - data: Includes datasets used to develop salinity response functions and evaluate salinity buffering capacity. Datasets for MEND model calibration. - database: Contains the `.dat` file required by PHREEQC for model execution. - README.md: A Markdown plain text file describing the computational tools and directories. Files are a mixture of plain text CSV (comma-separated value) and plain text *.dat files written by the model; no special software is required to read them.

EARTH SCIENCE > AGRICULTURE > SOILS > SOIL SALINIT↗

Stellar Calibration of the WIC and SI Imagers and the GEO Photometers on IMAGE/FUV

The FUV instrument on the IMAGE spacecraft comprises three wide-field imagers, the Wide-Band Imaging Camera (WIC) of observing N2 Lyman-Birge-Hopfield (LBH) (140-190 nm) emissions and the Spectrographic Imager (SI), which has a 121.8 nm channel for observing red-shifted HI Lya photons and a 135.6 run channel for observing 01 135.6 nm emissions. In addition, three HI Lya photometers (GEO) are used to monitor the geocorona. The fields of view are 17 degrees x 17 degrees for the WIC imagers, 15 degrees x 15 degrees for the two SI imagers, and 10 diameter for the three GEO photometers. As the IMAGE spacecraft spins every 120 seconds, the GEO photometers sweep out circles on the sky (at 0 degrees and plus or minus 30 degrees with respect to the spacecraft spin plane), and the WIC and SI imagers use the Time Delay Integration (TDI) method to construct images centered on the Earth. Many FUV-bright stars are seen in the WIC, SI and even the GEO data. WE have used archived International Ultraviolet Explorer (IUE) far-ultraviolet flux spectra for 22 of the brightest of these stars to help refine the FUV instrumental sensitivities. The stars chosen range in spectral type form B0V to A11V, with magnitudes ranging from V- 1.3 (a Cru) to V=4.7 (G Cen) (although many more fainter stars are also seen). The initial results of this stellar calibration will be presented and compared with the pre-flight and dayglow modeling results.

Gladstone, R.↗

Model Checking Failed Conjectures in Theorem Proving: A Case Study

Interactive mechanical theorem proving can provide high assurance of correct design, but it can also be a slow iterative process. Much time is spent determining why a proof of a conjecture is not forthcoming. In some cases, the conjecture is false and in others, the attempted proof is insufficient. In this case study, we use the SAL family of model checkers to generate a concrete counterexample to an unproven conjecture specified in the mechanical theorem prover, PVS. The focus of our case study is the ROBUS Interactive Consistency Protocol. We combine the use of a mechanical theorem prover and a model checker to expose a subtle flaw in the protocol that occurs under a particular scenario of faults and processor states. Uncovering the flaw allows us to mend the protocol and complete its general verification in PVS.

Pike, Lee↗

Comparative Study of Three Reconnection X Line Models at the Earth's Dayside Magnetopause Using in Situ Observations

This work examines the large-scale aspects of magnetic field reconnection at the Earth's dayside magnetopause. We use two sets of reconnection events, which are identified mostly by the in situ detection of accelerated and Alfvenic plasma flows. We intercompare three analytical models that predict the reconnection X line location and orientation, namely, the Trattner et al. (2007) and Swisdak and Drake (2007) models and also a modified version of the component merging model. In the first set of reconnection observations, we show three fortuitous, quasi-simultaneous dayside magnetopause crossing events where two widely separated spacecraft detect reconnection signatures, and the X line location and orientation can be inferred from the observations. We compare X line model predictions to those inferred from observations. These three reconnection events indicate the presence of an extended (greater than 7 Earth radii in length), component-type reconnection X line on Earth's dayside magnetopause connecting and structuring the reconnection signatures at locations far apart. In the second set of reconnection events, we analyze the X line models' performance in predicting the observed reconnection outflow direction, i.e., its north-south and/or east-west senses, in a total of 75 single, rather than multiple and quasi-simultaneous, magnetopause crossing events, where reconnection-associated plasma flows were clearly present. We found that the Swisdak and Drake's (2007) X line model performs slightly better, albeit not statistically significant, when predicting both accelerated plasma flow north-south and east-west components in 73% and 53% of the cases, respectively, as compared to the Trattner et al. (2007) model (70% north-south and 42% east-west) and the modified component merging model (66% north-south and 50% east-west).

Souza, V. M.↗

Predicting partner fitness based on spatial structuring in a light-driven microbial community

Microbial communities have vital roles in systems essential to human health and agriculture, such as gut and soil microbiomes, and there is growing interest in engineering designer consortia for applications in biotechnology ( e . g ., personalized probiotics, bioproduction of high-value products, biosensing). The capacity to monitor and model metabolite exchange in dynamic microbial consortia can provide foundational information important to understand the community level behaviors that emerge, a requirement for building novel consortia. Where experimental approaches for monitoring metabolic exchange are technologically challenging, computational tools can enable greater access to the fate of both chemicals and microbes within a consortium. In this study, we developed an in-silico model of a synthetic microbial consortia of sucrose-secreting Synechococcus elongatus PCC 7942 and Escherichia coli W. Our model was built on the NUFEB framework for Individual-based Modeling (IbM) and optimized for biological accuracy using experimental data. We showed that the relative level of sucrose secretion regulates not only the steady-state support for heterotrophic biomass, but also the temporal dynamics of consortia growth. In order to determine the importance of spatial organization within the consortium, we fit a regression model to spatial data and used it to accurately predict colony fitness. We found that some of the critical parameters for fitness prediction were inter-colony distance, initial biomass, induction level, and distance from the center of the simulation volume. We anticipate that the synergy between experimental and computational approaches will improve our ability to design consortia with novel function.

59 BASIC BIOLOGICAL SCIENCES↗

Dayside Aurora Dynamics

Images from the FUV (Far UltraViolet) instrument on board the IMAGE spacecraft will be presented to demonstrate the auroral dynamics in the dayside auroral zone and the polar cap region. optical emissions detected by three different detectors of FUV come from precipitations of energetic protons, electrons, and both species, respectively. In general, auroral activities in these regions responded very well to variations in the boundary conditions either external or internal to the magnetosphere, i.e., in the solar wind or the magnetotail. As a result, auroral images from FUV provide an excellent tool to investigate particle acceleration and transport processes within the geospace, such as shock acceleration, substorm injections, etc. we will interpret the observed auroral images using various models, discuss difference and similarity in the auroral activity from several typical cases, and assess conditions optimal to each type of auroral activity.

Spann, James F.↗

Polyunsaturated Fatty Acids Mend Macrophage Transcriptome, Glycome, and Phenotype in the Patients with Neurodegenerative Diseases, Including Alzheimer’s Disease

Macrophages of healthy subjects have a pro-resolution phenotype, upload amyloid-β (Aβ) into endosomes, and degrade Aβ, whereas macrophages of patients with Alzheimer’s disease (AD) generally have a pro-inflammatory phenotype and lack energy for brain clearance of Aβ. To clarify the pathogenesis of sporadic AD and therapeutic effects of polyunsaturated fatty acids (PUFA) with vitamins B and D and antioxidants on monocyte/macrophage (MM) migration in the AD brain, MM transcripts in energy and Aβ degradation, MM glycome, and macrophage clearance of Aβ. We followed for 31.3 months (mean) ten PUFA-supplemented neurodegenerative patients: 3 with subjective cognitive impairment (SCI), 2 with mild cognitive impairment (MCI), 3 MCI/vascular cognitive impairment, 2 with dementia with Lewy bodies, and 7 non-supplemented caregivers. We examined: monocyte migration in the brain and a blood-brain barrier model by immunochemistry and electron microscopy; macrophage transcriptome by RNAseq; macrophage glycome by N-glycan profiling and LTQ-Orbitrap mass spectrometry; and macrophage phenotype and phagocytosis by immunofluorescence. MM invade Aβ plaques, upload but do not degrade Aβ, and release Aβ into vessels, which develop cerebrovascular amyloid angiopathy (CAA); PUFA upregulate energy and Aβ degradation enzyme transcripts in macrophages; PUFA enhance sialylated N-glycans in macrophages; PUFA reduce oxidative stress and increase pro-resolution MM phenotype, mitochondrial membrane potential, and Aβ phagocytosis (p < 0.001). Macrophages of SCI, MCI, and AD patients have interrelated defects in the transcriptome, glycome, Aβ phagocytosis, and Aβ degradation. PUFA mend macrophage transcriptome, enrich glycome, enhance Aβ clearance, and benefit the cognition of early-stage AD patients.

60 APPLIED LIFE SCIENCES↗

Plasmaspheric Erosion via Plasmasphere Coupling to Ring Current Plasmas: EUV Observations and Modeling

During a geomagnetic storm on 24 May 2000, the IMAGE Extreme Ultraviolet (EUV) camera observed a plasmaspheric density trough in the evening sector at L-values inside the plasmapause. Forward modeling of this feature has indicated that plasmaspheric densities beyond the outer wall of the trough are well below model expectations. This diminished plasma condition suggests the presence of an erosion process due to the interaction of the plasmasphere with ring current plasmas. We present an overview of EUV, energetic neutral atom (ENA), and Far Ultraviolet (FUV) camera observations associated with the plasmaspheric density trough of 24 May 2000, as well as forward modeling evidence of the lie existence of a plasmaspheric erosion process during this period. FUV proton aurora image analysis, convolution of ENA observations, and ring current modeling are then presented in an effort to associate the observed erosion with coupling between the plasmasphere and ring-current plasmas.

Adrian, M. L.↗

Digital Tools for the Preventive Conservation of Built Heritage: The Church of Santa Ana in Seville

Historic Building Information Modelling (HBIM) plays a pivotal role in heritage conservation endeavours, offering a robust framework for digitally documenting existing structures and supporting conservation practices. However, HBIM’s efficacy hinges upon the implementation of case-specific approaches to address the requirements and resources of each individual asset and context. This paper defines a flexible and generalisable workflow that encompasses various aspects (i.e., documentation, surveying, vulnerability assessment) to support risk-informed decision making in heritage management tailored to the peculiar conservation needs of the structure. This methodology includes an initial investigation covering historical data collection, metric and condition surveys and non-destructive testing. The second stage includes Finite Element Method (FEM) modelling and structural analysis. All data generated and processed are managed in a multi-purpose HBIM model. The methodology is tested on a relevant case study, namely, the church of Santa Ana in Seville, chosen for its historical significance, intricacy and susceptibility to seismic action. The defined level of detail of the HBIM model is sufficient to inform the structural analysis, being balanced by a more accurate representation of the alterations, through linked orthophotos and a comprehensive list of alphanumerical parameters. This ensures an adequate level of information, optimising the trade-off between model complexity, investigation time requirements, computational burden and reliability in the decision-making process. Field testing and FEM analysis provide valuable insight into the main sources of vulnerability in the building, including the connection between the tower and nave and the slenderness of the columns.

Chaves, Estefanía↗

Summary of Quantitative Interpretation of Image Far Ultraviolet Auroral Data

Direct imaging of the magnetosphere by instruments on the IMAGE spacecraft is supplemented by simultaneous observations of the global aurora in three far ultraviolet (FUV) wavelength bands. The purpose of the multi-wavelength imaging is to study the global auroral particle and energy input from thc magnetosphere into the atmosphere. This paper describes provides the method for quantitative interpretation of FUV measurements. The Wide-Band Imaging Camera (WIC) provides broad band ultraviolet images of the aurora with maximum spatial and temporal resolution by imaging the nitrogen lines and bands between 140 and 180 nm wavelength. The Spectrographic Imager (SI), a dual wavelength monochromatic instrument, images both Doppler-shifted Lyman alpha emissions produced by precipitating protons, in the SI-12 channel and OI 135.6 nm emissions in the SI-13 channel. From the SI-12 Doppler shifted Lyman alpha images it is possible to obtain the precipitating proton flux provided assumptions are made regarding the mean energy of the protons. Knowledge of the proton (flux and energy) component allows the calculation of the contribution produced by protons in the WIC and SI-13 instruments. Comparison of the corrected WIC and SI-13 signals provides a measure of the electron mean energy, which can then be used to determine the electron energy fluxun-. To accomplish this reliable modeling emission modeling and instrument calibrations are required. In-flight calibration using early-type stars was used to validate the pre-flight laboratory calibrations and determine long-term trends in sensitivity. In general, very reasonable agreement is found between in-situ measurements and remote quantitative determinations.

Frey, H. U.↗

Measurement of precipitation induced FUV emission and Geocoronal Lyman Alpha from the IMI mission

This final report describes the activities of the Lockheed Martin Palo Alto Research Laboratory in studying the measurement of ion and electron precipitation induced Far Ultra-Violet (FUV) emissions and Geocoronal Lyman Alpha for the NASA Inner Magnetospheric Imager (IMI) mission. this study examined promising techniques that may allow combining several FUV instruments that would separately measure proton aurora, electron aurora, and geocoronal Lyman alpha into a single instrument operated on a spinning spacecraft. The study consisted of two parts. First, the geocoronal Lyman alpha, proton aurora, and electron aurora emissions were modeled to determine instrument requirements. Second, several promising techniques were investigated to determine if they were suitable for use in an IMI-type mission. Among the techniques investigated were the Hydrogen gas cell for eliminating cold geocoronal Lyman alpha emissions, and a coded aperture spectrometer with sufficient resolution to separate Doppler shifted Lyman alpha components.

Mende, Stephen B.↗

Constraining the Dense Matter Equation of State with New NICER Mass–Radius Measurements and New Chiral Effective Field Theory Inputs

Pulse profile modeling of X-ray data from the Neutron Star Interior Composition Explorer is now enabling precision inference of neutron star mass and radius. Combined with nuclear physics constraints from chiral effective field theory (χEFT), and masses and tidal deformabilities inferred from gravitational-wave detections of binary neutron star mergers, this has led to a steady improvement in our understanding of the dense matter equation of state (EOS). Here, we consider the impact of several new results: the radius measurement for the 1.42 M ⊙ pulsar PSR J0437−4715 presented by Choudhury et al., updates to the masses and radii of PSR J0740+6620 and PSR J0030+0451, and new χEFT results for neutron star matter up to 1.5 times nuclear saturation density. Using two different high-density EOS extensions—a piecewise-polytropic (PP) model and a model based on the speed of sound in a neutron star (CS)—we find the radius of a 1.4 M ⊙ (2.0 M ⊙ ) neutron star to be constrained to the 95% credible ranges ${12.28}_{-0.76}^{+0.50}$ km (${12.33}_{-1.34}^{+0.70}$ km) for the PP model and ${12.01}_{-0.75}^{+0.56}$ km (${11.55}_{-1.09}^{+0.94}$ km) for the CS model. The maximum neutron star mass is predicted to be ${2.15}_{-0.16}^{+0.14}$M ⊙ and ${2.08}_{-0.16}^{+0.28}$M ⊙ for the PP and CS models, respectively. We explore the sensitivity of our results to different orders and different densities up to which χEFT is used, and show how the astrophysical observations provide constraints for the pressure at intermediate densities. Moreover, we investigate the difference R 2.0 − R 1.4 of the radius of 2 M ⊙ and 1.4 M ⊙ neutron stars within our EOS inference.

gravitational wave sources↗

Spectroscopic comparison of effects of electron radiation on mechanical properties of two polyimides

The differences in the radiation durabilities of two polyimide materials, Du Pont Kapton and General Electric Ultem, are compared. An explanation of the basic mechanisms which occur during exposure to electron radiation from analyses of infrared (IR) and electron paramagnetic resonance (EPR) spectroscopic data for each material is provided. The molecular model for Kapton was, in part, established from earlier modeling for Ultem (pp. 1293-1298 of IEEE Transactions on Nuclear Science, December 1984). Techniques for understanding the durability of one complex polymer based on the understanding of a different and equally complex polymer are demonstrated. The spectroscopic data showed that the primary radiation-generated change in the tensile properties of Ultem (a large reduction in tensile elongation) was due to crosslinking, which followed the capture by phenyl radicals of hydrogen atoms removed from gem-dimethyl groups. In contrast, the tensile properties of Kapton remained unchanged because radical-radical recombination, a self-mending process, took place.

Long, Edward R., Jr.↗

Artificial auroras in the upper atmosphere. II - Imaging results

On the ATLAS 1 mission (STS-45, launched March 24, 1992) two experiments, AEPI (Atmospheric Emissions Photometric Imaging) and SEPAC (Space Experiments with Particle Accelerators) performed the first of a series of active experiments intended to probe the atmosphere, ionosphere and magnetosphere with electron beams. The luminous artificial aurora generated by the electron beam interaction was detected and measured by AEPI both in white light and in a narrow wavelength band at 427.8 nm (peak intensity 5 kR). Modelling calculation showed that there was a significant contribution from emissions originating near the spacecraft. The spatial intensity distribution of the observed auroral patch is consistent with emission contribution from both high and low altitude regions. An extended tail in the direction of the shuttle wake was observed in the 427.8 nm channel, consistent with a decay time associated with the dissipation of the hot electron plasma.

Mende, S. B.↗

Mending cracks atom-by-atom in rutile TiO2 with electron beam radiolysis

Abstract Rich electron-matter interactions fundamentally enable electron probe studies of materials such as scanning transmission electron microscopy (STEM). Inelastic interactions often result in structural modifications of the material, ultimately limiting the quality of electron probe measurements. However, atomistic mechanisms of inelastic-scattering-driven transformations are difficult to characterize. Here, we report direct visualization of radiolysis-driven restructuring of rutile TiO 2 under electron beam irradiation. Using annular dark field imaging and electron energy-loss spectroscopy signals, STEM probes revealed the progressive filling of atomically sharp nanometer-wide cracks with striking atomic resolution detail. STEM probes of varying beam energy and precisely controlled electron dose were found to constructively restructure rutile TiO 2 according to a quantified radiolytic mechanism. Based on direct experimental observation, a “two-step rolling” model of mobile octahedral building blocks enabling radiolysis-driven atomic migration is introduced. Such controlled electron beam-induced radiolytic restructuring can be used to engineer novel nanostructures atom-by-atom.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗