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The software contains objects that are building blocks for PV modeling and interactive data fitting based on: Optoelectronic models for tandem/multijunction solar cells including resistive and luminescent coupling; simulation of modules composed of 2T, 3T, and 4T tandem solar cells; and energy yield analysis of PV systems composed of tandem solar cells.
The workers at the Mayak nuclear facility near Ozyorsk, Russia are a primary source of information about exposure to radiation at low-dose rates, since they were subject to protracted exposures to external gamma rays and to internal exposures from plutonium inhalation. Here we re-examine lung cancer mortality rates and assess the effects of external gamma and internal plutonium exposures using recently developed Monte Carlo dosimetry systems. Using individual lagged mean annual lung doses computed from the dose realizations, we fit excess relative risk (ERR) models to the lung cancer mortality data for the Mayak Workers Cohort using risk-modeling software. We then used the corrected information matrix (CIM) approach to widen the confidence intervals of ERR by taking into account the uncertainty in doses represented by multiple realizations from the Monte Carlo dosimetry systems. Findings of this work revealed that there were 930 lung cancer deaths during follow-up. Plutonium lung doses (but not gamma doses) were generally higher in the new dosimetry systems than those used in the previous analysis. This led to a reduction in the risk per unit dose compared to prior estimates. The estimated ERR/Gy for external gamma-ray exposure was 0.19 (95% CI: 0.07 to 0.31) for both sexes combined, while the ERR/Gy for internal exposures based on mean plutonium doses were 3.5 (95% CI: 2.3 to 4.6) and 8.9 (95% CI: 3.4 to 14) for males and females at attained age 60. Accounting for uncertainty in dose had little effect on the confidence intervals for the ERR associated with gamma-ray exposure, but had a marked impact on confidence intervals, particularly the upper bounds, for the effect of plutonium exposure [adjusted 95% CIs: 1.5 to 8.9 for males and 2.7 to 28 for females]. In conclusion, lung cancer rates increased significantly with both external gamma-ray and internal plutonium exposures. Accounting for the effects of dose uncertainty markedly increased the width of the confidence intervals for the plutonium dose response but had little impact on the external gamma dose effect estimate. Adjusting risk estimate confidence intervals using CIM provides a solution to the important problem of dose uncertainty. This work demonstrates, for the first time, that it is possible and practical to use our recently developed CIM method to make such adjustments in a large cohort study.
Considerable advances have been made in battery safety models, but achieving predictive accuracy across a wide range of conditions continues to be challenging. Interactions between dynamically evolving mechanical, electrical, and thermal state variables make model prediction difficult during mechanical abuse scenarios. In this study, we develop a physics-based modeling approach that allows for choosing between different mechanical and electrochemical models depending on the required level of analysis. We demonstrate the use of this approach to connect cell-level abuse response to electrode-level and particle-level transport phenomena. A pseudo-two-dimensional model and simplified single-particle models are calibrated to electrical-thermal cycling data and applied to mechanically induced short-circuit scenarios to understand how the choice of electrochemical model affects the model prediction under abuse scenarios. These models are implemented using user-defined subroutines on ls-dyna finite element software and can be coupled with existing automotive crash safety models.
We describe and demonstrate an open-source algorithm for simultaneously quantifying degradation and soiling of photovoltaic (PV) systems from energy-production time series data. The new analysis is based on year-on-year degradation rate analysis combined with stochastic rate and recovery soiling analysis. The algorithm is designed to fit into the workflow provided by RdTools, a Python module maintained by NREL and collaboratively developed with the community, which provides a framework and functions for degradation and loss-factor analysis of PV field data. We demonstrate the method on numerically simulated PV data sets and show that it reduces the root-mean-square error of the P50 degradation rate estimate when soiling is present.
Supplementing an existing high-quality seismic monitoring network with openly available station data could improve coverage and decrease magnitudes of completeness; however, this can present challenges when varying levels of data quality exist. Without discerning the quality of openly available data, using it poses significant data management, analysis, and interpretation issues. Incorporating additional stations without properly identifying and mitigating data quality problems can degrade overall monitoring capability. If openly available stations are to be used routinely, a robust, automated data quality assessment for a wide range of quality control (QC) issues is essential. To meet this need, we developed Pycheron, a Python-based library for QC of seismic waveform data. Pycheron was initially based on the Incorporated Research Institutions for Seismology’s Modular Utility for STAtistical kNowledge Gathering but has been expanded to include more functionality. Pycheron can be implemented at the beginning of a data processing pipeline or can process stand-alone data sets. Its objectives are to (1) identify specific QC issues; (2) automatically assess data quality and instrumentation health; (3) serve as a basic service that all data processing builds on by alerting downstream processing algorithms to any quality degradation; and (4) improve our ability to process orders of magnitudes more data through performance optimizations. This article provides an overview of Pycheron, its features, basic workflow, and an example application using a synthetic QC data set.
The aim of this project is to develop software and hardware for fast real-time data processing and autonomous detector control and calibration for the sPHENIX and the future EIC experiments. Below summarizes Georgia Tech team efforts in the past year: 1. We developed a real-time clustering algorithm and FPGA-based pipeline architecture for processing fired pixel data from ALPIDE sensors in sPHENIX experiments. Our Columnar Clustering Co-Design introduces a hardware-aware, stream-friendly approach that segments pixel data by column pairs using a Column Pair Clustering (CPC) strategy, followed by Cluster Stitching to merge adjacent subclusters. Implemented in Vitis HLS, the pipeline comprises five stages—read-in, subclustering, stitching, analysis, and write-out—connected by tagged HLS streams with custom end-of-event signaling for robust synchronization. We designed a pipelined dataflow model optimized for throughput, low latency, and minimal buffering, enabling scalable clustering across events of arbitrary size. Our system maintains spatial precision via center-of-mass and shape key extraction and efficiently handles edge cases such as fragmented or nested clusters. Compared against DBSCAN in both software and hardware, our approach demonstrates competitive performance under FPGA constraints. 2. We also conducted a comprehensive algorithm-to-hardware co-design of connected component analysis tailored for sPHENIX experiments, focusing on real-time, low-latency processing using FPGAs and High-Level Synthesis (HLS). Starting from a Python-based particle tracking pipeline, the team translated the core logic—graph traversal via DFS and Union-Find—into an HLS-compatible C++ model, replacing dynamic memory and recursion with static arrays and pipelined control flow. The final design includes a fully streamed and dataflow-compatible Union-Find kernel optimized across five iterations, incorporating loop pipelining, array partitioning, AXI/FIFO interface tuning, and function flattening. Experimental results show up to 14.8× speedup over the CPU baseline, reducing per-graph latency to 1.58 μs and demonstrating strong resource efficiency with only ~7k LUTs and zero BRAM usage. The design maintains functional correctness against the Python reference using a Python-based C-simulation framework and Mean Squared Error metrics. This work validates the potential of HLS-driven FPGA designs for edge-level HEP data acquisition, laying a scalable foundation for future integration with real-time detector pipelines and multi-graph processing systems.
The Midwest Regional Carbon Sequestration Partnership (MRCSP) was founded in 2003 as part of the U.S. Department of Energy’s (DOE’s) Regional Carbon Sequestration Partnership initiative. Since its founding, MRCSP has made significant strides toward making CCUS a viable option for states in the region. The public/private consortium, funded through the DOE Regional Carbon Sequestration Initiative, brings together nearly 40 industry partners and 10 states. Battelle, as the project lead, oversees research, development and operations and coordinates activities among the partners. The incremental, phased approach has built a valuable knowledge base for the industry and paved the way for commercial-scale adoption of CCUS technologies. From 2008 to 2020, MRCSP Phase III focused on the development of large-scale injection projects. This report is part of a series of reports prepared under the Midwestern Regional Carbon Sequestration Partnership (MRCSP) Phase III (Development Phase). These reports summarize and detail the findings of the work conducted under the Phase III project. The report describes the regional analysis of the Northern Niagaran Pinnacle Reef Trend (NNPRT) in Northern Michigan as part of the MRCSP programs Regional Assessment goals. The goal of this task was to perform an initial assessment of the geologic storage capacity and injectivity of the Northern Fairway of Michigan’s Niagaran Reef Trend. This was achieved through three main objectives: 1) development of a reef atlas, 2) understanding the regional trends in geology, and 3) estimating CO 2 and CO 2 -EOR resources. Data collected across multiple subtasks were integrated into a mappable database that could be accessed from many of the leading software. The reef atlas was used to map the reefs and associated characteristics across the entire NNPRT. Several methodologies were explored to estimate the CO 2 and CO 2 -EOR resources across the trend which included three scenarios: 1) storage only using fluid substitution and volumetric estimations, 2) CO 2 -EOR which applied proximity analysis concepts and measured performance metrics from the Core Energy reefs to predict performance at all oil reefs, and 3) enhanced storage scenario which combined CO 2 -EOR with fluid substitution to represent maximized storage after completion of CO 2 -EOR.
The trigger selection capabilities of the ATLAS detector have been significantly enhanced for the LHC Run- 2 in order to cope with the higher event rates and with the large number of simultaneous interactions (pile-up) per protonproton bunch crossing. A new hardware system, designed to analyse real time event-topologies at Level-1 came to full use in 2017. A hardware-based track reconstruction system, expected to be used real-time in 2018, is designed to provide track information to the high-level software trigger at its full input rate. The high-level trigger selections are largely relying on offline-like reconstruction techniques, and in some cases multivariate analysis methods. Despite the sudden change in LHC operations during the second half of 2017, which caused an increase in pile-up and therefore also in CPU usage of the trigger algorithms, the set of triggers (so called trigger menu) running online has undergone only minor modifications thanks to the robustness and redundancy of the trigger system, and the use of a levelling luminosity scheme in agreement with LHC and other experiments. Here, this presentation gives a brief yet comprehensive review of the real-time performance of the ATLAS trigger system in 2017. Considerations will be presented on the most relevant parameters of the trigger (efficiency to collect signal and output data rate) as well as details on some aspects of the algorithms which are run real-time on the High Level Trigger CPU farm.
There is an increased interest in topologically nontrivial magnetic spin textures such as skyrmions and chiral domain-wall solitons, both from a point of fundamental physics understanding as well as potential technological interest in low-power memory applications. In order to control their behavior, it is necessary to understand their complex spin texture at the nanoscale. Lorentz transmission electron microscopy (LTEM) is a suitable technique for studying these systems due to its high spatial resolution and capability to simultaneously characterize magnetic texture and microstructure. In this work, we present the application of PyLorentz, an open-source software suite that we have developed, for quantitative image analysis of Neel-type skyrmions in thin-film heterostructures. PyLorentz enhances LTEM capabilities by enabling reconstruction of magnetic induction maps from experimental images, as well as simulating LTEM images using micromagnetic simulation data. We demonstrate this for simulated Neel skyrmions as well as experimental data from [Pt/Co/W] multilayer heterostructures. Finally, we also show how simulation-assisted LTEM analysis is crucial for understanding these complex magnetic spin textures, in which the reconstructed magnetic induction map (seen in the LTEM images) differs significantly from the magnetization configuration.
XPS of Si/GaN photocathode after 10 hour chronoamperometry (CA) testing. Surface chemical composition and valence band structure of GaN were obtained by X-ray photoemission spectroscopy (XPS) on a Kratos Axis Ultra DLD system at a takeoff angle of 0° relative to the surface normal. An Al Kα source (hν = 1486.6 eV) was used to excite the core level electrons. Pass energy of 20 eV was used for the narrow scan of core levels and valence band spectra, and step size of 0.05 eV and 0.025 eV, respectively. The Spectral fitting was conducted using CasaXPS analysis software. The binding energy scales of all core levels were corrected to the N 1s of Ga – N bond at 397.8 eV. XPS O1s core level spectra from 10 hours CA tested Si/GaN sample, and deconvolution shows O - Ga bond, O - N - Ga bond and OH - H2O bond.
XPS of Si/GaN photocathode after 4 hour chronoamperometry (CA) testing. Surface chemical composition and valence band structure of GaN were obtained by X-ray photoemission spectroscopy (XPS) on a Kratos Axis Ultra DLD system at a takeoff angle of 0° relative to the surface normal. An Al Kα source (hν = 1486.6 eV) was used to excite the core level electrons. Pass energy of 20 eV was used for the narrow scan of core levels and valence band spectra, and step size of 0.05 eV and 0.025 eV, respectively. The Spectral fitting was conducted using CasaXPS analysis software. The binding energy scales of all core levels were corrected to the N 1s of Ga – N bond at 397.8 eV. XPS O1s core level spectra from 4 hour CA tested Si/GaN sample, and deconvolution shows O - Ga bond, O - N - Ga bond and OH - H2O bond.
NOODLES is a new cross-domain collaborative visualization and analysis capability being developed at NREL. The NOODLES specification is a minimal protocol that can tie different software packages and platforms together. As an example, a simulation code that speaks this protocol could stream iso-surfaces to an immersive VR space and a web browser. Another example is a team (with some members across the country) classifying and discovering features in a statistical data plot, driven from a researcher's existing Python-based workflow. In this talk, we will discuss some background on the problems that this protocol intends to solve, basic principles of the specification, the current state of supporting libraries, and some demonstrations of the protocol in action.
Metaproteomics is an increasingly popular methodology that provides information regarding the metabolic functions of specific microbial taxa and has potential for contributing to ocean ecology and biogeochemical studies. A blinded multi-laboratory intercomparison was conducted to assess comparability and reproducibility of taxonomic and functional results and their sensitivity to methodological variables. Euphotic zone samples from the Bermuda Atlantic Time-series Study (BATS) in the North Atlantic Ocean collected by in situ pumps and the autonomous underwater vehicle (AUV) Clio were distributed with a paired metagenome, and one-dimensional (1D) liquid chromatographic data-dependent acquisition mass spectrometry analysis was stipulated. Analysis of mass spectra from seven laboratories through a common bioinformatic pipeline identified a shared set of 1056 proteins from 1395 shared peptide constituents. Quantitative analyses showed good reproducibility: pairwise regressions of spectral counts between laboratories yielded R 2 values averaged 0.62±0.11, and a Sørensen similarity analysis of the top 1000 proteins revealed 70 %–80 % similarity between laboratory groups. Taxonomic and functional assignments showed good coherence between technical replicates and different laboratories. A bioinformatic intercomparison study, involving 10 laboratories using eight software packages, successfully identified thousands of peptides within the complex metaproteomic datasets, demonstrating the utility of these software tools for ocean metaproteomic research. Lessons learned and potential improvements in methods were described. Future efforts could examine reproducibility in deeper metaproteomes, examine accuracy in targeted absolute quantitation analyses, and develop standards for data output formats to improve data interoperability. Together, these results demonstrate the reproducibility of metaproteomic analyses and their suitability for microbial oceanography research, including integration into global-scale ocean surveys and ocean biogeochemical models.
Abstract Bacterial DNA methylation is involved in diverse cellular functions, including modulation of gene expression, DNA repair, and restriction–modification systems for defense against viruses and other foreign DNA. Restriction systems hinder efforts to engineer organisms to produce fuels and chemicals from waste and renewable feedstocks by degrading DNA during transformation. Methylome analysis allows identification of motifs within a bacterial chromosome that may be targeted by native restriction enzymes. Further expression of the corresponding methyltransferases in Escherichia coli allows plasmid DNA to be protected from restriction in the target organism, thereby drastically enhancing transformation efficiency. Nanopore sequencing can detect methylated bases, but software is needed to transform modified base coordinates into methylated motifs. Here, we develop MIJAMP (MIJAMP Is Just A MethylBED Parser), a software package that was developed to discover methylated motifs from the output of ONT’s Modkit or other data in the methylBED format. MIJAMP employs a human-driven refinement strategy that empirically validates all motifs against genome-wide methylation data, thus eliminating incorrect motifs. MIJAMP also reports methylation data on specific, user-defined motifs. Using MIJAMP, we determined the methylated motifs both in a control strain (wild-type E. coli) and in Synecococcus sp. strain PCC7002, laying the foundation for improved transformation in this organism. MIJAMP is available at https://code.ornl.gov/alexander-public/mijamp/. One Sentence Summary: Here we describe software written to discover DNA methylation motifs from nanopore sequencing data.
Abstract We present the EpIC Monte Carlo event generator for exclusive processes based on generalised parton distributions. EpIC utilises the PARTONS framework, which provides a flexible software architecture and a variety of modelling options for the partonic description of the nucleon. The generator offers a comprehensive set of features, including simulation of a variety of exclusive processes and radiative corrections. It may be used both in the analysis of experimental data, as well as for impact studies, especially for the future electron-ion colliders.
Asteroseismology is an exceptional tool for studying stars using the properties of observed modes of oscillation. So far the process of performing an asteroseismic analysis of a star has remained somewhat esoteric and inaccessible to nonexperts. In this software paper we describe PBjam, an open-source Python package for analyzing the frequency spectra of solar-like oscillators in a simple but principled and automated way. The aim of PBjam is to provide a set of easy-to-use tools to extract information about the radial and quadropole oscillations in stars that oscillate like the Sun, which may then be used to infer bulk properties such as stellar mass, radius, age, or even structure. Asteroseismology and its data analysis methods are becoming increasingly important as space-based photometric observatories are producing a wealth of new data, allowing asteroseismology to be applied in a wide range of contexts such as exoplanet, stellar structure and evolution, and Galactic population studies.
This package contains field data, modeling files, and scripts supporting the investigation of the drivers of streamflow intermittency in an urbanized catchment. It includes the field data collected from electrical resistivity tomography (ERT) surveys, distributed temperature sensing (DTS), continuous self-potential (SP) monitoring, groundwater and stilling well. In addition, it contains the data and results of the coupled water- and electrical-flow model developed using the COMSOL Multiphysics and Advanced Terrestrial Simulator (ATS), as well as software files and Jupyter notebooks used to process the data and generate figures in the manuscript submitted for peer review. The data archive is organized in the following directories: 1) Climate Includes hourly precipitation and daily evapotranspiration time series (2024 – 2025) provided as CSV files, alongside a text file detailing dataset units. 2) Coupled_model Field_Application subfolder contains the ATS XML input scripts, data files, output data for the SP site. It also contains the Jupyter notebook (Plot_final_calib.ipynb) to visualize the results of the modeled SP, stream-groundwater exchange and moisture content. The flow model simulation is executed using the ATS XML scripts and the included Python script (generate_data_set.py) to convert ATS output to COMSOL-ready input. COMSOL Multiphysics template (.m can only be used with COMSOL with MATLAB) is executed using the ATS output data to simulate the potential field. 3) Discharge Includes the electrical conductivity (EC) time series (provided as CSV files) from salt slug injections. It also includes the Jupyter notebook (Discharge_process.ipynyb) used to estimate discharge. All discharge measurements collated into rating_curve_processed.csv 4) DTS Contains collated DTS data including raw Stokes and anti-Stokes measurement (provided as .h5 file). It also includes DTS processing.ipynb, a Jupyter notebook for calibrating the DTS data using dts_calibration Python package. cooler_calibration.csv is the DTS calibration CSV used in the calibration sequence. 5) ERT Contains raw resistivity data (provided as CSV files), spatial location of each of the electrodes (provided as CSV files), and files used for the resistivity inversion. 6) Slug_test Includes the slug test data at all the groundwater wells provided as CSV files, as well as the Jupyter notebook (Slug_test.ipynb) for calculating hydraulic conductivity. 7) SP Contains the SP data collected in field at the SP sites (provided as CSV files). 8) Well_data Contains two subfolders: 1) Raw, which provides unprocessed pressure, electrical conductivity and temperature timeseries downloaded from the loggers in all the groundwater and stilling wells, and 2) Processed, which contains sorted, QA/QC timeseries data for each well. The data archive also contains data_process.ipynb, a Jupyter notebook used for field data analysis and generating figures (plotting well, SP, climate, and discharge data, as well as calculating head gradient at sites with nested groundwater wells). Note: Code files (.ipynb, .py, .xml) can be opened in any standard code editor, .exo file can be viewed using Paraview, .h5 files can be opened using HDFView software and h5py Python package, and .resipy file can be opened with the open-source ResIPy software.
In this study, we present PyKrev, a Python library for the analysis of complex mixture Fourier transform mass spectrometry (FT-MS) data. PyKrev is a comprehensive suite of tools for analysis and visualization of FT-MS data after formula assignment has been performed. These comprise formula manipulation and calculation of chemical properties, intersection analysis between multiple lists of formulas, calculation of chemical diversity, assignment of compound classes to formulas, multivariate analysis, and a variety of visualization tools producing van Krevelen diagrams, class histograms, PCA score, and loading plots, biplots, scree plots, and UpSet plots. The library is showcased through analysis of hot water green tea extracts and Scotch whisky FT-ion cyclotron resonance-MS data sets. PyKrev addresses the lack of a single, cohesive toolset for researchers to perform FT-MS analysis in the Python programming environment encompassing the most recent data analysis techniques used in the field.