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Field and Model Data Associated with the Manuscript “Drivers of Streamflow Intermittency in Humid Regions: 1. Evaluating Above- and Below-ground Controls of Flow Persistence in a Forested Catchment”

This package contains field data, modeling files, and scripts supporting the investigation of the drivers of streamflow intermittency in a forested catchment. It includes the field data collected from electrical resistivity tomography (ERT) surveys, ground penetrating radar (GPR), continuous self-potential (SP) monitoring, electromagnetic (EM) imaging, 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 Contains two subfolders: Synthetic and Field_Application subfolder. Synthetic subfolder contains the ATS XML input script (can be opened using any code editor) for the four synthetic hydrological cases tested (Connected and gaining, Connected and losing, Disconnected and losing, and dry stream). It also includes other experimental cases to test the influence of precipitation and concentration gradient. For each synthetic case, 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 (.mph can be opened with the commercial software COMSOL and requires a license) is executed using the ATS output data to simulate the potential field. It also includes the Synthetic_model_plot.ipynb (can be opened using any code editor) to visualize the SP result and generate manuscript figures. The data subfolder contains mesh files to run both the ATS (.exo and .stl files can be viewed using Paraview; .h5 files can be opened using HDFView software and h5py Python package) and COMSOL models. Field_Application subfolder contains two subfolders: ES_MDA_inversion and Final_Model. ES_MDA_inversion contains the Python script (.py can be opened using any code editor) and SP observation data used to run the Ensemble Smoother with Multiple Data Assimilation (ES-MDA) inversion sequence to get the optimal model parameters. The Final_model subfolder contains the ATS XML input scripts, data files, output data for the two SP sites. The same workflow steps outlined for the Synthetic subfolder apply here. It also contains the Jupyter notebook (Plot_final_calib.ipynb) to visualize the results of the modeled SP, stream-groundwater exchange and moisture content. 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) EM Contains the CSV file of the EM data from the DUALEM-42, including spatial coordinates (x, y, z), apparent conductivity, and in-phase measurements at 2 m coil separations for horizontal coplanar (HCP) and perpendicular (PRP) geometries. 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 (.resipy can be opened with the open-source ResIPy software). 6) GPR Includes GPR field datasets collected at 100 MHz and 250 MHz antenna frequencies, along with the processing/interpretation project file (GPR_process.gpz can be viewed using EKKO_Project 6, a commercial software by Sensors & Software that requires a license). 7) 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. 8) SP Contains the SP data collected in field at the two SP sites (one in the perennial reach and the other in the intermittent reach), provided as DAT files. 9) 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). It also includes DTW.ipynb, a Jupyter notebook containing the code for the dynamic time warping (DTW) with sliding window to evaluate SP signal synchronicity.

ATS↗

Deep Water Impact Ensemble Data Set

Asteroids of various sizes, speeds, and compositions are zipping around the solar system with potential future Earth engagements. Most of the earth is covered in ocean and impacts would likely occur in deep ocean water. The IEEE SciVis Contest 2018 is dedicated to the visualization and analysis of simulations designed to study asteroid impacts in deep ocean water.

"asteroid impact" meteor "in situ" visualization↗

Real-Time Observation of Molecular Spinning with Angular High-Harmonic Spectroscopy

We demonstrate an angular high-harmonic spectroscopy method to probe the spinning dynamics of a molecular rotation wave packet in real time. With the excitation of two time-delayed, polarization-skewed pump pulses, the molecular ensemble is impulsively kicked to rotate unidirectionally, which is subsequently irradiated by another delayed probe pulse for high-order harmonic generation (HHG). The spatiotemporal evolution of the molecular rotation wave packet is visualized from the time-dependent angular distributions of the HHG yields and frequency shift measured at various polarization directions and time delays of the probe pulse. Here, the observed frequency shift in HHG is demonstrated to arise from the nonadiabatic effect induced by molecular spinning. Different from the previous spectroscopic and Coulomb explosion imaging techniques, the angular high-harmonic spectroscopy method can reveal additionally the electronic structure and multiple orbitals of the sampled molecule. All the experimental findings are well reproduced by numerical simulations. Further extension of this method would provide a powerful tool for probing complex polyatomic molecules with HHG spectroscopy.

74 ATOMIC AND MOLECULAR PHYSICS↗

The Parallel System for Integrating Impact Models and Sectors (pSIMS)

We present a framework for massively parallel climate impact simulations: the parallel System for Integrating Impact Models and Sectors (pSIMS). This framework comprises a) tools for ingesting and converting large amounts of data to a versatile datatype based on a common geospatial grid; b) tools for translating this datatype into custom formats for site-based models; c) a scalable parallel framework for performing large ensemble simulations, using any one of a number of different impacts models, on clusters, supercomputers, distributed grids, or clouds; d) tools and data standards for reformatting outputs to common datatypes for analysis and visualization; and e) methodologies for aggregating these datatypes to arbitrary spatial scales such as administrative and environmental demarcations. By automating many time-consuming and error-prone aspects of large-scale climate impacts studies, pSIMS accelerates computational research, encourages model intercomparison, and enhances reproducibility of simulation results. We present the pSIMS design and use example assessments to demonstrate its multi-model, multi-scale, and multi-sector versatility.

crop modeling↗

Integrated hydrogeophysical modelling and data assimilation for geoelectrical leak detection

Time-lapse electrical resistivity tomography (ERT) measurements provide indirect observations of hydrological processes in the Earth's shallow subsurface at high spatial and temporal resolution. ERT has been used in the past decades to detect leaks and monitor the evolution of associated contaminant plumes. Specifically, inverted resistivity images allow visualization of the dynamic changes in the structure of the plume. However, existing methods do not allow the direct estimation of leak parameters (e.g. leak rate, location, etc.) and their uncertainties. We propose an ensemble-based data assimilation framework that evaluates proposed hydrological models against observed time-lapse ERT measurements without directly inverting for the resistivities. Each proposed hydrological model is run through the parallel coupled hydro-geophysical simulation code PFLOTRAN-E4D to obtain simulated ERT measurements. The ensemble of model proposals is then updated using an iterative ensemble smoother. In this paper, we demonstrate the proposed framework on synthetic and field ERT data from controlled tracer injection experiments. Our results show that the approach allows joint identification of contaminant source location, initial release time, and solute loading from the cross-borehole time-lapse ERT data, alongside with an assessment of uncertainties in these estimates. We demonstrate a reduction in site-wide uncertainty by comparing the prior and posterior plume mass discharges at a selected image plane. This framework is particularly attractive to sites that have previously undergone extensive geological investigation (e.g., nuclear sites). It is well suited to complement ERT imaging and we discuss practical issues in its application to field problems.

58 GEOSCIENCES↗

Mechanical Regulation of Photosynthesis in Cyanobacteria

Photosynthetic organisms regulate their responses to many diverse stimuli in an effort to balance light harvesting with utilizable light energy for carbon fixation and growth (source–sink regulation). This balance is critical to prevent the formation of reactive oxygen species that can lead to cell death. However, investigating the molecular mechanisms that underlie the regulation of photosynthesis in cyanobacteria using ensemble-based measurements remains a challenge due to population heterogeneity. Here, to address this problem, we used long-term quantitative time-lapse fluorescence microscopy, transmission electron microscopy, mathematical modelling and genetic manipulation to visualize and analyse the growth and subcellular dynamics of individual wild-type and mutant cyanobacterial cells over multiple generations. We reveal that mechanical confinement of actively growing Synechococcus sp. PCC 7002 cells leads to the physical disassociation of phycobilisomes and energetic decoupling from the photosynthetic reaction centres. We suggest that the mechanical regulation of photosynthesis is a critical failsafe that prevents cell expansion when light and nutrients are plentiful, but when space is limiting. These results imply that cyanobacteria must convert a fraction of the available light energy into mechanical energy to overcome frictional forces in the environment, providing insight into the regulation of photosynthesis and how microorganisms navigate their physical environment.

BASIC BIOLOGICAL SCIENCES,BIOMASS FUELS↗

An uncertainty visualization framework for large-scale cardiovascular flow simulations: A case study on aortic stenosis

We present a generalizable uncertainty quantification (UQ) and visualization framework for lattice Boltzmann method simulations of high Reynolds number vascular flows, demonstrated on a patient-specific stenosed aorta. The framework combines EasyVVUQ for parameter sampling with large-eddy simulation turbulence modeling in HemeLB, and executes ensembles on the Frontier exascale supercomputer. Spatially resolved metrics, including entropy and isosurface-crossing probability, are used to map uncertainty in pressure and wall shear stress fields directly onto vascular geometries. Two sources of model variability are examined: inlet peak velocity and the Smagorinsky constant. Inlet velocity variation produces high uncertainty downstream of the stenosis where turbulence develops, while upstream regions remain stable. Smagorinsky constant variation has little effect on the large-scale pressure field but increases WSS uncertainty in localized high-shear regions. In both cases, the stenotic throat manifests low entropy, indicative of robust identification of elevated WSS. By linking quantitative UQ measures to three-dimensional anatomy, the framework improves interpretability over conventional 1D UQ plots and supports clinically relevant decision-making, with broad applicability to vascular flow problems requiring both accuracy and spatial insight.

Hemodynamics↗

Large Ensemble Analytic Framework for Consequence-Driven Discovery of Climate Change Scenarios

An analytic scenario generation framework is developed based on the idea that the same climate outcome can result from very different socioeconomic and policy drivers. The framework builds on the Scenario Matrix Framework’s abstraction of “challenges to mitigation” and “challenges to adaptation” to facilitate the flexible discovery of diverse and consequential scenarios. We combine visual and statistical techniques for interrogating a large factorial data set of 33,750 scenarios generated using the Global Change Assessment Model. We demonstrate how the analytic framework can aid in identifying which scenario assumptions are most tied to user-specified measures for policy relevant outcomes of interest, specifically for our example high or low mitigation costs. We show that the current approach for selecting reference scenarios can miss policy relevant scenario narratives that often emerge as hybrids of optimistic and pessimistic scenario assumptions. We also show that the same scenario assumption can be associated with both high and low mitigation costs depending on the climate outcome of interest and the mitigation policy context. In the illustrative example, we show how agricultural productivity, population growth, and economic growth are most predictive of the level of mitigation costs. Formulating policy relevant scenarios of deeply and broadly uncertain futures benefits from large ensemble-based exploration of quantitative measures of consequences. To this end, we have contributed a large database of climate change futures that can support “bottom-up” scenario generation techniques that capture a broader array of consequences than those that emerge from limited sampling of a few reference scenarios.

54 ENVIRONMENTAL SCIENCES↗

From chiral anomaly to two-fluid hydrodynamics for electronic vortices

Highlights: • Chiral transformations with account for chiral anomaly were applied to the CDW model. • Two-fluid hydrodynamics was constructed of the order parameter and the normal liquid. • Topologically nontrivial dynamics appears under applied fields or charge injection. • Spontaneous spacetime vorticity under the driving current was modeled numerically. • Periodic sequence of amplitude nodes with 2π phase increments was demonstrated. - Abstract: Many recent experiments addressed manifestations of electronic crystals, particularly the charge density waves, in nano-junctions, under electric field effect, at high magnetic fields, together with real space visualizations by STM and micro X-ray diffraction. This activity returns the interest to stationary or transient states with static and dynamic topologically nontrivial configurations: electronic vortices as dislocations, instantons as phase slip centers, and ensembles of microscopic solitons. Describing and modeling these states and processes calls for an efficient phenomenological theory which should take into account the degenerate order parameter, various kinds of normal carriers and the electric field. Here we notice that the commonly employed time-depend Ginzburg–Landau approach suffers with violation of the charge conservation law resulting in unphysical generation of particles which is particularly strong for nucleating or moving electronic vortices. We present a consistent theory which exploits the chiral transformations taking into account the principle contribution of the fermionic chiral anomaly to the effective action. The resulting equations clarify partitions of charges, currents and rigidity among subsystems of the condensate and normal carriers. On this basis we perform the numerical modeling of a spontaneously generated coherent sequence of phase slips – the spacetime vortices – serving for the conversion among the injected normal current and the collective one.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Model-Free Data Authentication for Cyber Security in Power Systems

With the development and wide deployment of measurement equipment, data can be automatically measured and visualized for situation awareness in power systems. However, the cyber security of power systems is also threated by data spoofing attacks. This letter proposed a measurement data source authentication (MDSA) algorithm based on feature extraction techniques including ensemble empirical mode decomposition (EEMD) and fast Fourier transform (FFT), and machine learning for real-time measurement data classification. Compared with previous work, the proposed algorithm can achieve higher accuracy of MDSA using a shorter window of data from closely located synchrophasor measurement sensors.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Lithium Metal Battery Quality Control via Transformer–CNN Segmentation

Lithium metal battery (LMB) has the potential to be the next-generation battery system because of its high theoretical energy density. However, defects known as dendrites are formed by heterogeneous lithium (Li) plating, which hinders the development and utilization of LMBs. Non-destructive techniques to observe the dendrite morphology often use X-ray computed tomography (XCT) to provide cross-sectional views. To retrieve three-dimensional structures inside a battery, image segmentation becomes essential to quantitatively analyze XCT images. This work proposes a new semantic segmentation approach using a transformer-based neural network called TransforCNN that is capable of segmenting out dendrites from XCT data. In addition, we compare the performance of the proposed TransforCNN with three other algorithms, U-Net, Y-Net, and E-Net, consisting of an ensemble network model for XCT analysis. Our results show the advantages of using TransforCNN when evaluating over-segmentation metrics, such as mean intersection over union (mIoU) and mean Dice similarity coefficient (mDSC), as well as through several qualitatively comparative visualizations.

Quenum, Jerome (ORCID:0000000271265853)↗

Digital image filtering in visualized boundary layers

The application of two-dimensional low-pass matched filtering is presented for use in objective processing of digitized flow visualization images in order to identify instantaneous large-scale organized structures in turbulent boundary layers. The images were digitally acquired simultaneously with the outputs of a two-dimensional rake of hot-wire sensors in the field of view of the digital camera. Two-dimensional low wavenumber analysis brought out patterns in the visualization images which consisted of slender inclined structures having an average streamwise scale of 100-200 v/u (tau) and a length on the order of 1-2 delta. The similarly processed two-dimensional streamwise velocity reconstructions reveal similar features. The ensemble statistics indicate that these inclined features brought out by this processing may be a basic flow module in higher Reynolds number flows which links the so-called wall 'bursting' process and the larger outer scale motions.

Corke, T. C.↗

Revealing the atomic ordering of binary intermetallics using in situ heating techniques at multilength scales

Ordered intermetallic nanoparticles are promising electrocatalysts with enhanced activity and durability for the oxygen-reduction reaction (ORR) in proton-exchange membrane fuel cells (PEMFCs). The ordered phase is generally identified based on the existence of superlattice ordering peaks in powder X-ray diffraction (PXRD). However, after employing a widely used postsynthesis annealing treatment, we have found that claims of “ordered” catalysts were possibly/likely mixed phases of ordered intermetallics and disordered solid solutions. In this work, we employed in situ heating, synchrotron-based, X-ray diffraction to quantitatively investigate the impact of a variety of annealing conditions on the degree of ordering of large ensembles of Pt 3 Co nanoparticles. Monte Carlo simulations suggest that Pt 3 Co nanoparticles have a lower order–disorder phase transition (ODPT) temperature relative to the bulk counterpart. Furthermore, we employed microscopic-level in situ heating electron microscopy to directly visualize the morphological changes and the formation of both fully and partially ordered nanoparticles at the atomic scale. In general, a higher degree of ordering leads to more active and durable electrocatalysts. The annealed Pt 3 Co/C with an optimal degree of ordering exhibited significantly enhanced durability, relative to the disordered counterpart, in practical membrane electrode assembly (MEA) measurements. The results highlight the importance of understanding the annealing process to maximize the degree of ordering in intermetallics to optimize electrocatalytic activity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

PCMDI PMP Interactive Visualization Web Page, Atmospheric River Metrics

We present an open-source Python-based framework that can be used for objective evaluation of Atmospheric Rivers (ARs) in climate models. With a comprehensive pool of pre-defined metrics, this package is useful for systematic AR evaluation across a range of model simulations, such as the MIPs in CMIP5/6 models and large ensemble experiments.

Dong, Bo↗

PySFD: comprehensive molecular insights from significant feature differences detected among many simulated ensembles

Motivation Many modeling analyses of molecular dynamics (MD) simulations are based on a definition of states that can be (groups of) clusters of simulation frames in a feature space composed of molecular coordinates. With increasing dimension of this feature space (due to the increasing size or complexity of a simulated molecule), it becomes very difficult to cluster the underlying MD data and estimate a statistically robust model. To mitigate this “curse of dimensionality”, one can reduce the feature space, e.g., with principal component or time-lagged independent component analysis transformations, focusing the analysis on the most important modes of transitions. In practice, however, all these reduction strategies may neglect important molecular details that are susceptible to experimental verification. Results To recover such molecular details, I have developed PySFD (Significant Feature Differences analyzer for Python), a multi-processing software package that efficiently selects significantly different features of any user-defined feature type among potentially many different simulated state ensembles, such as meta-stable states of a Markov State Model (MSM). Applying PySFD on MSMs of an aggregate of 300 microseconds MD simulations recently performed on the major histocompatibility complex class II (MHCII) protein, I demonstrate how this toolkit can extract and visualize valuable mechanistic information from big MD simulation data, e.g., in form of networks of dynamic interaction changes connecting functionally relevant sites of a protein complex.

Biochemistry & Molecular Biology↗

Atomic-scale dynamics of a model glass-forming metallic liquid: Dynamical crossover, dynamical decoupling, and dynamical clustering

The phase behavior of multi-component metallic liquids is exceedingly complex because of the convoluted many-body and many-elemental interactions. Herein, we present systematic studies of the dynamic aspects of such a model ternary metallic liquid Cu 40 Zr 51 Al 9 using molecular dynamics simulation with embedded atom method. We observed a dynamical crossover from Arrhenius to super-Arrhenius behavior in the transport properties (diffusion coefficient, relaxation times, and shear viscosity) bordered at T x ~1300K. Unlike in many molecular and macromolecular liquids, this crossover phenomenon occurs in the equilibrium liquid state well above the melting temperature of the system (T m ~ 900K), and the crossover temperature is roughly twice of the glass-transition temperature (T g ). Below T x , we found the elemental dynamics decoupled and the Stokes-Einstein relation broke down, indicating the onset of heterogeneous spatially correlated dynamics in the system mediated by dynamic communications among local configurational excitations. To directly characterize and visualize the correlated dynamics, we employed a non-parametric, unsupervised machine learning technique and identified dynamical clusters of atoms with similar atomic mobility. The revealed average dynamical cluster size shows an accelerated increase below T x and mimics the trend observed in other ensemble averaged quantities that are commonly used to quantify the spatially heterogeneous dynamics such as the non-Gaussian parameter and the four-point correlation function.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗