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Well-balanced reconstruction techniques have been developed for stellar hydrodynamics to address the challenges of maintaining hydrostatic equilibrium during evolution. I show how to adapt a simple well-balanced method to the piecewise parabolic method for hydrodynamics. A python implementation of the method is provided.
Speciated volatile organic compounds (VOCs) were measured using an Ionicon PTR-TOF 8000 from 20 June to 3 July 2022 at the TRACER ancillary (TRACER ANC) site in Guy, TX. The dataset is reported at 1-min time resolution. Mixing ratios (ppb) are provided for acetone, methanol, acetaldehyde, dimethyl sulfide (DMS), furan, isoprene, methyl vinyl ketone plus methyl ethyl ketone (MVK + MEK), terpenes, xylene, and trimethylbenzene. Instrument calibrations for these species were performed weekly using a certified gas standard.
Data used in Figures
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The repository folder contains spreadsheets and script for soil greenhouse gas (GHG) fluxes, soil moisture, soil temperature, air temperature, and precipitation measurements collected from the Tropical Responses to Altered Climate Experiment (TRACE) at the Sabana Research Field Station, El Yunque National Forest (USDA Forest Service; 18°19′28.74″ N, 65°43′50.09″ W) — an open-air field warming experiment located in a lowland tropical forest in Puerto Rico within the Luquillo Experimental Forest (LEF) — six to seven years after Hurricanes Irma and Maria (2017). All spreadsheets for soil and air microclimate data, as well as soil greenhouse gas data, are included as csv files. Air temperature data are also included as Excel spreadsheets (.xlsx). The script is built in R Studio, which is the only software required to run data analysis. This dataset is associated with the manuscript “Larocca Conte G ; Zuvela L ; Cruz-Pérez R ; Barreto-Vélez T ; Becerra-Santillan N ; Campbell S ; Chu H ; Dam T ; Grullón-Penkova I ; Kleit M ; Ortiz-Iglesias D ; Rubio-Lebrón L ; Cavaleri M ; Reed S ; Sihi D ; Wood T ; O'Connell C., 2026. Lowland Tropical Forests Remain a Methane Sink Under Warming and Long-Term Hurricane Disturbance Recovery. Agricultural and Forest Meteorology. In review". The dataset was used to test the effect of warming on soil CH4 dynamics following long-term legacy effects of hurricane disturbance. The dataset includes: - An overall README file in word and pdf format describing methodology and spreadsheets’ structure. - Continuous measurements of soil temperature and moisture from January 2023 to July 2024 measured with Campbell CS655 probes (“TRACE_soil_temperature_and_moisture_2023_cleaned(in).csv” and “TRACE_soil_temperature_and_moisture_2024_cleaned. csv”). - Air temperature data measured with a HOBO MX23O1A data logger (“Hobo air temperature 2023 Sep 2024” and “Hobo air temperature 2023 Sep 2024” – “CSV FILES folders”). - Precipitation data from a nearby weather tower downloaded from González et al. (2025; “sabana_2020-2025.csv”). - Soil CH4 and CO2 effluxes measured intermittently in two summer campaigns (June – August 2023 and June – July 2024) with a LI-COR 8200-01S Portable Smart Chamber coupled with a LI-COR LI-7810 CH4/ CO2/H2O Trace Gas Analyzer (“23_24COMBO2.0.csv”). - R markdown script for data analysis (“Trace new_PLOTS.Rmd”).
The US nuclear industry is looking to improve on the operating economics of the current fleet of light-water reactors (LWRs). One way of achieving this is by operating fuel to higher burnup. In pressurized water reactors (PWRs), relaxing the current burnup limit will allow for cycle length extensions and power uprates; in boiling water reactors (BWRs) it may allow for improved fuel utilization and reduced feed assemblies, as well as more efficient power uprates and increased capacity factors that will support the Administration’s Executive Order to facilitate 5 GW of power uprates at existing nuclear facilities. However, one of the key limitations to operating fuel to higher burnup is the risk of fuel fragmentation, relocation, and dispersal (FFRD). Recognizing the high interest in extending burnup limits, the US Nuclear Regulatory Commission (NRC) has issued Draft Regulatory Guide DG-1434, which defines an approach that would be acceptable to the NRC for addressing FFRD risk. The approach defined will require better understanding of the phenomena leading to FFRD as well as best-estimate simulation methods to understand FFRD risk in high-burnup cores. The Nuclear Energy Advanced Modeling and Simulation program is supporting the FFRD industry challenge problem through development of state-of-the-art, high-fidelity modeling and simulation LWR analysis capabilities; namely, the BISON fuel performance code and the VERA core simulator software. These tools, along with the US NRC TRACE system analysis code, have been utilized for analysis of FFRD risk in both PWR and BWR cores in recent years. The work documented in this report addresses the lack of high-fidelity research for BWRs and builds on a previous activity where the framework has been applied to Cycles 16 through 18 of Limerick Unit 1, a BWR/4, with introduction of 8 high-burnup lead use assemblies (HBLUAs) that were representative of the 8 HBLUAs loaded into Limerick Unit 2 in 2021. VERA was used in this previous activity to model rod-by-rod depletion in these cycles, and its solution was used to initialize a TRACE simulation of a large-break loss-of-coolant accident (LBLOCA) at the end of Cycle 18. In the work documented in this report, the TRACE model was improved by refining the core mesh and utilizing a new feature that allows for capturing the full 3D VERA power distribution in the model. This allows for a more detailed solution for setting BISON boundary conditions. Furthermore, the solutions from VERA and TRACE were used to set up and perform BISON simulations of about 1,000 rods sampled from the core, including all burnup levels. Utilizing two cladding burst models, it was shown that no fuel rods were predicted to burst during the postulated LBLOCA transient. Additionally, a sensitivity study was performed by artificially increasing linear heat rate during the postulated LBLOCA to identify parameters that correlate with rod burst susceptibility. Burnup, fission gas release, and hoop strain were all found to be positively correlated with rod burst susceptibility. Small-break loss-of-coolant accident (SBLOCA) analyses were also performed; these analyses predicted cladding temperature increases that were bounded by the LBLOCA cladding temperatures for all small break sizes studied for this plant. However, future refinements to the plant response assumptions during the SBLOCA could impact the predicted cladding response. Finally, a benchmark study was performed between CTF and TRACE for LOCA conditions to better qualify CTF for BWR LOCA modeling.
The microscopic properties of atomic nuclei are used to study various scientific questions. They are essential for understanding the fundamental forces of nature and the chemical evolution of the universe. Detecting decay radiation from radioactive nuclei makes it possible to probe these fundamental nuclear properties. Detector waveform traces may contain additional information about the radiation. Generally, advanced signal processing techniques are needed to extract this additional information, often involving fitting the waveform with model response functions using non-linear least-squares optimization with second-order gradient methods. While this is a powerful technique, it is also computationally expensive, leading to slow processing time, which scales with the volume of data. To address this problem, we have developed a machine learning (ML) approach that infers the characteristics of traces from a model detector response function. In particular, we are interested in classifying whether a single recorded trace consists of one or two pulse constituents and estimating the pulse parameters. Furthermore, our proposed ML method can precisely extract the pulses’ parameters, such as energy and timing information, and accurately classify the pulse multiplicity of a trace. Unlike non-learning-based approaches, our ML approach uses neural networks that are significantly faster at inference, as they do not require any optimization during this stage.
Metal–organic framework (MOF)-based electrical impedance sensors are a growing class of sensors that show utility in the detection of environmentally toxic gases. Detection of trace NH 3 has been particularly difficult to design due to the low electrical response of NH 3 . However, this has been circumvented by judiciously selecting a MOF that has enhanced electrical response to NH 3 due to coadsorption with predominant atmospheric gases such as water. Herein, an MOF Cu(cyhdc) based sensor has been successfully demonstrated for the enhanced detection of environmentally toxic NH 3 gas. The sensor shows a change in impedance when it is exposed to 5 ppm of NH 3 . At 20 °C, >30% relative humidity (RH) is necessary to elicit a change, with the response increasing with RH and reaching 3170× at 92% RH, producing the largest published response to NH 3 for a MOF direct electrical sensor. In the absence of water, no change is observed toward 5 ppm of NH 3 over 20–50 °C. Here, this electrical response is largely driven by huge decreases in the imaginary component of the impedance, attributed to increased capacitance at the surface of the MOF crystallites upon NH 3 and H 2 O coadsorption. Complementary structural and microstructural characterization proves that the Cu(cyhdc) crystalline structure and morphology remain intact under trace NH 3 and/or H 2 O adsorption. Despite extremely low NH 3 , loadings seen in TGA, XPS, and FT-IR confirm NH 3 and H 2 O adsorption, and changes to the metal-carboxylate IR peak positions are observed upon NH 3 adsorption. Concentrated primarily at the outer surfaces of the MOF crystallites, this NH 3 and H 2 O coadsorption effectively increases the surface capacitance across the Cu(cyhdc) powder and enables direct electrical detection of trace NH 3 . Together, these results demonstrate how coadsorption of specific molecules (H 2 O) can be used to enable the electrical detection of trace toxic gases that would otherwise not have produced a MOF sensor response.
Complete characterization of unknowns via proteomics remains challenging. There exist regions of mass spectrometry-based proteomics data where empirical measurements are not attributed to peptides, and/or sequenced peptides from mass spectra are not attributed to any source. These uncharacterized regions are known as the “dark” proteome. Many proteomics tools rely on some a priori knowledge of sample composition; few tools allow for investigation of unknowns without relying on composition assumptions. Further, the potential low abundance of minor traces in these uncharacterized regions can make elucidation of the “dark” proteome challenging. Herein, we describe the development and evaluation of approaches to study the “dark” proteome and move towards an untargeted approach for more complete characterization, namely by studying minor human protein traces in non-human samples and combining that approach with non-human source organism identification without relying on assumptions. Human protein markers, in the form of genetically variant peptides, have been extensively examined in a variety of human matrices, including blood, plasma, and hair, but have yet to be investigated in non-human samples, such as cell cultures, as human contaminant traces. Genetically variant peptides are those that are found in proteins carrying single nucleotide polymorphisms. In this work, we aimed to (1) investigate the feasibility of detecting human contaminant genetically variant peptides (GVPs) in a diverse set of non-human organisms using public proteomics data and a computational pipeline, as well as to (2) develop a combined capability for untargeted source organism characterization and GVP detection. To our knowledge, this is the first report of applying these approaches towards a more complete proteomic characterization of unknowns. We successfully demonstrate the feasibility of broad human contaminant GVP detection in proteomics data, develop a better understanding of GVP detectability, characterize the sample-to-sample variability in GVP detection, and identify a core set of GVPs that can potentially be used as markers indicative of the human contaminant traces portion of the “dark” proteome. Further, we developed and evaluated a combined pipeline, MARLOWE-GVP, that enables both untargeted source organism characterization and GVP detection. We show high accuracy of correct source organism characterization and high degree of similarity of human contaminant GVP detection compared to the conventional approach. Success on both these efforts have allowed us to advance our understanding and characterization of the “dark” proteome.
Quantifying methane emissions is essential for meeting near-term climate goals and is typically carried out using methane concentrations measured downwind of the source. One major source of methane that is important to observe and promptly remediate is fugitive emissions from oil and gas production sites but installing methane sensors at the thousands of sites within a production basin is expensive. In recent years, relatively inexpensive metal oxide sensors have been used to measure methane concentrations at production sites. Current methods used to calibrate metal oxide sensors have been shown to have significant shortcomings, resulting in limited confidence in methane concentrations generated by these sensors. To address this, we investigate using machine learning (ML) to generate a model that converts metal oxide sensor output to methane mixing ratios. To generate test data, two metal oxide sensors, TGS2600 and TGS2611, were collocated with a trace methane analyzer downwind of controlled methane releases. Over the duration of the measurements, the trace gas analyzer’s average methane mixing ratio was 2.40 ppm with a maximum of 147.6 ppm. The average calculated methane mixing ratios for the TGS2600 and TGS2611 using the ML algorithm were 2.42 ppm and 2.40 ppm, with maximum values of 117.5 ppm and 106.3 ppm, respectively. A comparison of histograms generated using the analyzer and metal oxide sensors mixing ratios shows overlap coefficients of 0.95 and 0.94 for the TGS2600 and TGS2611, respectively. Overall, our results showed there was a good agreement between the ML-derived metal oxide sensors’ mixing ratios and those generated using the more accurate trace gas analyzer. This suggests that the response of lower-cost sensors calibrated using ML could be used to generate mixing ratios with precision and accuracy comparable to higher priced trace methane analyzers. This would improve confidence in low-cost sensors’ response, reduce the cost of sensor deployment, and allow for timely and accurate tracking of methane emissions.
The nuclear industry is investigating the feasibility of transitioning from 18- to 24-month fuel cycles because of the positive impact it would have on the operational costs for the current fleet of light-water reactors. A challenge to making this change is the increased risk of fuel fragmentation, relocation, and dispersal (FFRD) due to the known potential for ceramic fuel to pulverize into fine particles at the higher discharge burnups. Previous work has been performed by the Nuclear Energy Advanced Modeling and Simulation program to assess FFRD risk in high-burnup cores using the BISON fuel performance code and a coarse mesh thermal hydraulics (T/H) solution for a loss-of-coolant accident (LOCA) using the TRACE system T/H code. Because of the importance of the T/H solution for FFRD assessment, this study seeks to investigate the impact of using higher-fidelity subchannel techniques for modeling of the LOCA transient. CTF was used to model a subregion of a high-burnup core that was depleted by the Virtual Environment for Reactor Applications (VERA) multiphysics core simulator. Both coarse-mesh and pin-resolved models were created in CTF, and a consistent coarse-mesh TRACE model was also developed to allow for benchmarking the code results. Further, a large-break loss-of-coolant accident (LBLOCA) reflood transient was simulated using these three models, and results were compared. Results showed some consistent differences between the CTF and TRACE coarse models, including a higher peak cladding temperature (PCT) prediction in CTF and later quenching in CTF; however, the transient clad temperature behavior was similar, and these differences are likely due to post-critical heat flux heat transfer modeling differences and minimum film boiling temperature model differences. The pin-resolved results indicate that the PCT in the lumped model is often under-predicted by as much as 70 °C and that PCT occurs at a different location than the high-power pin in the assembly. The lumped model predicts a difference of 10 °C or less between the average and hot pins in the assembly, whereas the pin-resolved model predicts a range of over 100 °C. These results indicate that higher-fidelity T/H results may have an impact on predicted core behavior during LOCA, which may be important to consider when assessing FFRD risk.
The sources of the magmas that formed the Rustenburg Layered Suite of the Bushveld Complex in South Africa remain debated, despite decades of research. Vertical and lateral variation in bulk rock and mineral separate Sr-Nd isotopic compositions, which generally indicate enriched sources, demonstrate that the layered sequence was formed by the emplacement of multiple batches of magma, crucially resulting in episodes of PGE-Cr-V mineralisation. The Lu-Hf isotope compositions of zircon are, however, at odds with the bulk rock Sr-Nd isotopic heterogeneity as they show near homogeneous compositions throughout the layered sequence (εHf (2.06 Ga) =−8). This lack of variation in Hf isotope composition has been attributed to deep, continental lithospheric mantle-related and/or crustal contamination of plume-derived Bushveld magmas. In this study, we analysed the major, trace element and Sr-Nd isotope geochemistry of apatite in the Rustenburg Layered Suite. Apatite occurs as an intercumulus mineral in the lowermost regions and a cumulus mineral in the uppermost regions of the layered sequence and can therefore be used to test existing models for the isotopic disequilibrium between bulk rock Sr-Nd and zircon Hf isotopic compositions. Apatite is largely chlorapatite in the lowermost regions and fluorapatite in the uppermost regions of the layered sequence. The Merensky Reef is unusual in that it comprises both chlorapatite and fluorapatite. Apatite throughout the layered sequence is generally unzoned and shows no evidence of late-stage alteration. Trace element data show that apatite is enriched in L/HREE, with common negative Eu-Sr anomalies. These trace element signatures are consistent with a magmatic origin for the apatite grains, with prior, or concurrent, plagioclase crystallization from the same melt. Variability in in situ Sr and Nd isotope compositions of apatite is recorded throughout the layered sequence with εNd (2.06 Ga) compositions varying between −2.5 and − 10.2 and initial 87 Sr/ 86 Sr compositions varying between 0.7079 and 0.7103 (for the Marikana dikes only). The variability in Sr-Nd isotope compositions of apatite is consistent with the bulk rock (and mineral separate) variation in Sr-Nd isotope compositions, suggesting apatite preserves primary magmatic compositions in the Rustenburg Layered Suite.
Constructed wetlands are artificial ecosystems designed to replicate natural wetland processes. Microbial communities play a pivotal role in cycling essential elements, particularly sulfur, which is crucial for trace metal fixation and remobilization in these ecosystems. By their response to their environment, microbial communities act as biological indicators of the wetland performance. To address knowledge gaps pertinent to the changes in trace metal bioavailability in relation to microbial activities in the H-02 constructed wetland, we performed this study to investigate temporal and spatial variations in microbial communities by using molecular biology tools. Quantitative polymerase chain reaction and next generation sequencing techniques were employed to analyze archaeal and bacterial groups associated with sulfur and methane cycling. Alpha diversity indices were used to assess species richness, evenness, and dominance. Results indicated high gene abundance of Desulfuromonas (5.37 × 10 6 g.cell –1 ), methane oxidizing bacteria (6.92 × 10 6 g.cell –1 ), and methanogenic microorganisms (3.02 × 10 5 g.cell –1 ) during cool months. Warm months were marked by sulfate reducing bacteria dominance (3.31 × 10 6 g.cell –1 ), potentially due to competitive interactions and environmental conditions, higher temperatures, and lower redox potential. Spatial variability among microbial groups was insignificant, but trends in gene abundance indicated complex factors influencing these groups. Next generation sequencing data demonstrated Firmicutes as the most abundant phylum with over 50% regardless of the season or sampling location. Cool months exhibited higher alpha diversity than warm months. Overall, this study showed that seasonal changes significantly impacted the microbial communities in the H-02 constructed wetland that are associated with the sulfur cycle and eventually trace metal biogeochemistry, revealing two distinct mechanisms of the sulfur cycle between the two main seasons, whereas spatial variability effects were not conclusive.
Chemical synthesis of Li 3 N through lithium nitridation has potential to advance rechargeable battery and nitrogen fixation technology. However, studies of the conditions for forming Li 3 N on the lithium surface via nitrogen gas exposure report contradictory findings, such as the spontaneous reaction of Li with pure N 2 , the impossibility of forming Li 3 N through pure Li and N 2 interaction, the requirement of trace H 2 O to catalyze the reaction, and evidence to the contrary. In this study, ambient pressure X-ray photoelectron spectroscopy (APXPS) was applied to evaluate the in situ chemical evolution of the lithium metal surface under nitrogen gas up to 800 mTorr. At pressures ≤10 mTorr, no Li 3 N was detected. At higher pressures, surface Li 3 N rapidly reacts with trace CO 2 . Additionally, because metallic lithium is readily oxidized by trace gases, the atomic nitrogen concentration of the lithium surface remains below 2%. When nitridation follows oxidation by O 2 gas, CO 2 gas, or H 2 O vapor, surface Li 3 N formation is inhibited. These results suggest that nitrogen gas can diffuse through the oxidized lithium metal surface to react with subsurface metallic lithium.
Anomalous transport of multi-species plasma is considered with the generalized Hasegawa–Wakatani model [A. R. Knyazev and S. I. Krasheninnikov, Phys. Plasmas 31, 012502 (2024)] further extended to incorporate the Finite Larmor Radius (FLR) effects. By introducing the “associated” enstrophy, it is shown that with no FLR effects (where anomalous transport of all ion species is described as a transport of passive scalars in the turbulent fields of the electrostatic potential and electron density fluctuations) the fluctuating densities of ion species converge to the state where they are linearly proportional to electron density and vorticity fluctuations, which confirm previous numerical findings of [A. R. Knyazev and S. I. Krasheninnikov, Phys. Plasmas 31, 012502 (2024)]. However, in contrast to the “cold” ion approximation, with the FLR effects included, both the plasma turbulence and the dynamics of all ion species become interconnected. Therefore, for simplicity, the FLR effects in this work were considered only for a small “trace” impurity fraction. It is found that for light (neon) “trace” impurity, the FLR effects reduce both anomalous flux and density fluctuations. However, for heavy (tungsten) “trace” impurity, the FLR effects exhibit non-monotonic impact on anomalous transport.