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Hyporheic-zone Processes and Stream Oxygen Dynamics: Insights from a Multiscale Reactive Transport Model: Modeling Archive
This archive contains the data and Python scripts required to reproduce the analyses and figures in the study: Gomez-Velez, J. D., Rathore, S. S., Cohen, M. J., & Painter, S. L. (2025). Hyporheic-zone Processes and Stream Oxygen Dynamics: Insights from a Multiscale Reactive Transport Model. Submitted to Water Resources Research. The analysis utilizes the subgrid model Advection Dispersion Equation with Lagrangian Subgrids (ADELS) implemented in the Advanced Terrestrial Simulator (ATS; https://amanzi.github.io/ats/stable/). In this case, the ATS and Amanzi versions are (1) ATS version 1.5.1_f5ba18f8 and (2) Amanzi version 1.6-dev_53444cca4. The repository includes a Jupyter Notebook and the necessary data (Pandas DataFrames stored as pickle files) to generate the figures for the manuscript. Additionally, it contains Python scripts to create ATS input files, run the ATS simulations, and post-process the results. Finally, it provides routines for parameter estimation using the Single-Station Metabolism (SSM) model with the Differential Evolution Adaptive Metropolis (DREAM) Markov Chain Monte Carlo (MCMC) algorithm with ZS enhancements (DREAM-ZS).
Efficient Berry phase calculation via adaptive variational quantum computing approach
We present an adaptive variational quantum algorithm to estimate the Berry phase accumulated by a nondegenerate ground state under cyclic, adiabatic evolution of a time-dependent Hamiltonian. Our method leverages cyclic adiabatic evolution of the Hamiltonian and employs adaptive variational quantum algorithms for state preparation and evolution, optimizing circuit efficiency while maintaining high accuracy. We benchmark our approach on dimerized Fermi–Hubbard chains with four sites, demonstrating precise Berry phase simulations in both noninteracting and interacting regimes. Our results show that circuit depths reach up to 106 layers for noninteracting systems and increase to 279 layers for interacting systems due to added complexity. In addition, we demonstrate the robustness of our scheme across a wide range of parameters governing adiabatic evolution and variational algorithms. These findings highlight the potential of adaptive variational quantum algorithms for advancing quantum simulations of topological materials and computing geometric phases in strongly correlated systems.
Recent Progress in Solid‐State Lithium Batteries through Cathode Microstructure Engineering
A high‐performance cathode is necessary to realize the great potentials of solid‐state batteries such as high energy density and long cycle life. It is also needed to validate electrolyte performance, which is lacking. Currently, cathodes for solid‐state batteries are thinner and have lower cathode active material content than their lithium‐ion battery counterpart, resulting from insufficient conductivity and limiting the battery energy density. This review article provides an overview of recent development in cathode microstructures and their impact on battery properties, including compatibility between cathode and electrolyte, cathode architecture design, interface engineering, correlation between material properties, cathode processing approaches, and performance, as well as the advanced characterization methods used to understand the above correlations . Some perspectives on future development are shared including utilizing in situ and operando characterization tools to better understand dynamic evolution of the cathode/electrolyte interface, adapting artificial intelligence and machine learning to design and optimize cathode structures. The article is aimed to promote research interest on cathode development and advance solid‐state battery technologies.
Krylov Subspace Methods for Quantum Dynamics with Time-Dependent Generators
Krylov subspace methods in quantum dynamics identify the minimal subspace in which a process unfolds. To date, their use is restricted to time evolutions governed by time-independent generators. Here, we introduce a generalization valid for driven quantum systems governed by a time-dependent Hamiltonian that maps the evolution to a diffusion problem in a one-dimensional lattice with nearest-neighbor hopping probabilities that are inhomogeneous and time dependent. This representation is used to establish a novel class of fundamental limits to the quantum speed of evolution and operator growth. We also discuss generalizations of the algorithm, adapted to discretized time evolutions and periodic Hamiltonians, with applications to many-body systems.
Functional Nano-to-Microstructures by Jet Printing and Direct Ink Writing
Jet-based printing techniques and direct ink writing have emerged as complementary, convergent technologies serving as key platforms in additive manufacturing for functional nano- to microscale architectures. This review highlights how these approaches enable fine feature resolution and three-dimensional structures in advanced electronics and biointerfacing applications. The interplay of fluid mechanics, viscoelastic ink rheology, droplet–substrate interactions, and drying dynamics is examined as a critical determinant of printing fidelity. Application-focused case studies, from flexible thin-film transistors to bioprinted artificial tissues, demonstrate how precise structural control via printing translates to enhanced device performance and new functionality in electronic and biological systems. Finally, we discuss the challenges and future opportunities driving the evolution of these printing platforms toward autonomous, adaptive, and intelligent manufacturing systems.
Climate change drives convergent evolution of root traits on Sky Island climate relicts
Roots are essential to the strategies plants use to survive in variable environments, yet we know little of how they vary within species. Experimental conditions demonstrate that intraspecific plant root traits respond strongly to variation in the environment; however, it is unclear when these responses can be characterized as evolution in response to selective pressures of climate change over many generations. Sky Islands are model, natural climate relict ecosystems to examine climate-change driven evolution. Utilizing a common garden with replicate genotypes of Populus angustifolia (Narrowleaf cottonwood) from six Sky Island (SI) populations and nine adjacent Mountain Chain (MC) populations across three genetic provenances, we hypothesized that SI root traits have diverged due to historical isolation in warmer, drier climates. When grown in common conditions, populations originating on SI’s showed convergent evolution across three distinct genetic provenances, which was characterized by 44.16% decreased total root length, 42.64% decreased average root volume, 43.31% decreased root surface area, and significantly less root trait variation, relative to adjacent mountain chains. Convergent evolution of root traits from trees originating on SI’s is correlated with changes in mean annual precipitation and potential evapotranspiration in the field over the past ~ 125 years. These results demonstrate a consistent pattern in root trait evolution at the landscape scale and the role of climate on the evolution of root traits in a genetic and geographic context relevant to climate change.
Monitoring Fracture Hydromechanical Evolution in the Lab and Field Using Unsupervised Metric Learning
Fractures evolve in time through thermal‐hydraulic‐mechanical‐chemical (THMC) processes that alter their long‐range hydraulic transport properties and modify subsurface behavior and activities. The location of subsurface fractures makes it necessary to use remote sensing techniques such as passive or active seismic monitoring for fracture characterization. In this paper, we develop a machine learning approach to monitor the evolution of fracture properties using passive seismic sources in a laboratory setting and using active seismic monitoring from the Sanford Underground Research Facility in Lead, South Dakota, at a depth of 1.25 km in amphibolite rock during stimulation of natural fractures as well as during induced fracturing. The unsupervised metric learning technique applies tandem neural networks (twin (Siamese) or triplet) with contrastive loss and adaptive margins to track slowly varying systems for which class or similarity labels are not available. The approach adopts locality‐sensitive hashing to divide time‐ordered contiguous data into an arbitrary number of pseudo‐classes. Contrastive‐loss training with many hash bins generates an evolving latent‐space trajectory. This approach enables unsupervised metric learning for seismic data stacks under the condition of contiguous state sampling and slowly varying fracture properties. The displacement discontinuity theory provides a mechanistic foundation for the fracture‐dependent trajectories that are related to relaxation of fractures with time‐dependent specific stiffness responding to changes in stress or fluid saturation.
Resilient Entanglement Distribution in a Multihop Quantum Network
The evolution of quantum networking requires architectures capable of dynamically reconfigurable entanglement distribution to meet diverse user needs and ensure tolerance against transmission disruptions. We introduce multihop quantum networks to improve network reach and resilience by enabling quantum communications across intermediate nodes, thus broadening network connectivity and increasing scalability. We present multihop two-qubit polarization-entanglement distribution within a quantum network at the Oak Ridge National Laboratory campus. Our system uses wavelength-selective switches for adaptive bandwidth management on a software-defined quantum network that integrates a quantum data plane with classical data and control planes, creating a flexible, reconfigurable mesh. Our network distributes entanglement across six nodes within three subnetworks, each located in a separate building, optimizing quantum state fidelity and transmission rate through adaptive resource management. Additionally, we demonstrate the network's resilience by implementing a link recovery approach that monitors and reroutes quantum resources to maintain service continuity despite link failures—paving the way for scalable and reliable quantum networking infrastructures.
Development of Automated Atom Probe Tomography capability to study the influence of applied voltage and laser power on the final apparent composition of the analyzed specimen
This study presents the development and implementation of an autonomous Bayesian optimization (BO) framework for controlling and optimizing experimental parameters in Atom Probe Tomography (APT). Using commercial silicon needle samples as a benchmark system, we demonstrate that BO can efficiently navigate the complex parameter space of voltage and laser power to achieve target charge state ratios (specifically Si + /(Si + +Si 2+ )) with minimal experimental evaluations. Our implementation integrates Gaussian Process modeling with the CAMECA atom probe control framework, enabling autonomous adjustment of experimental conditions in real-time. Results show that the algorithm successfully converges to target ratios under different scenarios: maintaining a reference ratio, increasing the ratio (favoring Si 1+ ), and decreasing the ratio (favoring Si 2+ ). The system adapts to specimen evolution during analysis, compensating for changes in apex geometry while maintaining optimization targets. This work establishes a proof of concept for AI-driven optimization in APT, addressing the traditional challenges of manual parameter tuning and paving the way for applications to more complex materials where compositional accuracy is critical.
Coupling Microstructural Evolution Simulations to Material Property Degradation Predictions for Plasma-Facing Materials
Reliable material performance is required for plasma-facing material (PFM) candidates. Previous research has shown that plasma and neutron radiation exposure induces microstructural changes in PFMs; changes in thermal and electrical conductivities and in material hardening and embrittlement were also observed after neutron irradiation. These material property changes will negatively impact the performance of the PFMs in a fusion reactor. Despite the well-known connection between material microstructure, properties, and performance, there is a need for validated modeling capabilities connecting PFM property degradation with microstructural evolution under fusion-relevant conditions. We are developing a simulation capability to couple plasma-induced microstructural evolution to material property degradation. Our approach relies on deliberate mapping between individual simulation models and experimental characterization for validation. The open-source Multiphysics Object-Oriented Simulation Environment (MOOSE) software was used for this simulation capability development. A MOOSE phase-field model was coupled with the cluster dynamics code, Xolotl, to predict microstructural evolution. Microstructure characterization techniques, including scanning electron microscopy (SEM), transmission electron microscopy (TEM), and laser scanning confocal microscopy (LSCM) are used to validate these microstructural evolution simulations. Calculation of thermal and electrical conductivities with first principles simulations was performed for bulk material and for grain boundaries; these results are used within MOOSE models to calculate effective thermal and electrical conductivities as a function of grain characteristics. Thermoreflectance and four-probe techniques were employed to measure the thermal and electrical conductivities, respectively. A MOOSE crystal plasticity model was adapted to predict microstructure-sensitive deformation behavior, and X-ray diffraction (XRD) was used to collect bulk dislocation density data for validation. After individual simulation validation, these models are coupled to predict material property changes resulting from plasma exposure. We focused here on an experimental design to emphasize the separate effects of moderate thermal loads and plasma exposure using tungsten. Annealing of tungsten was performed under a protective environment for temperatures ranging from 500 C to 1500 C. The plasma exposure was completed in the Tritium Plasma Experiment at Idaho National Laboratory under a deuterium flux of 1e22 D/m^2-s. This incremental approach is employed to build confidence in the modeling capability: separate-effects tests ensure that the models capture key mechanisms from single environmental conditions before predicting PFM property degradation under combined loads. We will show our early results from coupling these simulation models to predict PFM property changes from microstructural evolution. Comparisons of the simulation results with preliminary validation data will be discussed.
From Reproducible Edge–Cloud Experimentation to Real-World Practice: The E2Clab Experience
Reproducibility is already difficult in distributed systems; on the computing continuum, it becomes substantially harder. Applications that span sensing devices, edge and fog resources, and cloud platforms must be evaluated across heterogeneous hardware, variable network conditions, cross-layer orchestration decisions, and long-running workflow lifecycles. We use E2Clab as a case study to examine these challenges and their implications for experimental methodology. We explain why reproducible experimentation is harder on the continuum, then revisit E2Clab as an initial response based on explicit modeling of infrastructure, workflow lifecycle, and artifacts. Lastly, we discuss how its evolution toward more realistic application settings can be understood through the lens of Translational Computer Science. We argue that reproducible continuum experimentation requires methods that are rigorous enough for research while remaining adaptable to real-world practice.
Connect microstructure evolution to property degradation with validated simulation
Reliable material performance is required for plasma-facing material (PFM) candidates. Previous research has shown that plasma and neutron radiation exposure induces microstructural changes in PFMs; changes in thermal and electrical conductivities and in material hardening and embrittlement were also observed after neutron irradiation. These material property changes will negatively impact the performance of the PFMs in a fusion reactor. Despite the well-known connection between material microstructure, properties, and performance, there is a need for validated modeling capabilities connecting PFM property degradation with microstructural evolution under fusion-relevant conditions. We are developing a simulation capability to couple plasma-induced microstructural evolution to material property degradation. Our approach relies on deliberate mapping between individual simulation models and experimental characterization for validation. The open-source Multiphysics Object-Oriented Simulation Environment (MOOSE) software was used for this simulation capability development. A MOOSE phase-field model was coupled with the cluster dynamics code, Xolotl, to predict microstructural evolution. Microstructure characterization techniques, including scanning electron microscopy (SEM), transmission electron microscopy (TEM), and laser scanning confocal microscopy (LSCM) are used to validate these microstructural evolution simulations. Calculation of thermal and electrical conductivities with first principles simulations was performed for bulk material and for grain boundaries; these results are used within MOOSE models to calculate effective thermal and electrical conductivities as a function of grain characteristics. Thermoreflectance and four-probe techniques were employed to measure the thermal and electrical conductivities, respectively. A MOOSE crystal plasticity model was adapted to predict microstructure-sensitive deformation behavior, and X-ray diffraction (XRD) was used to collect bulk dislocation density data for validation. After individual simulation validation, these models are coupled to predict material property changes resulting from plasma exposure. We focused here on an experimental design to emphasize the separate effects of moderate thermal loads and plasma exposure using tungsten. Annealing of tungsten was performed under a protective environment for temperatures ranging from 500$^o$C to 1500$^o$C. The plasma exposure was completed in the Tritium Plasma Experiment at Idaho National Laboratory under a deuterium flux of 1e22 $\frac{D}{m^2s}$. This incremental approach is employed to build confidence in the modeling capability: separate-effects tests ensure that the models capture key mechanisms from single environmental conditions before predicting PFM property degradation under combined loads. We will show our early results from coupling these simulation models to predict PFM property changes from microstructural evolution. Comparisons of the simulation results with preliminary validation data will be discussed.
Genomic analysis of Klebsiella aerogenes circulating in New Mexico
Klebsiella aerogenes is an opportunistic pathogen and a growing cause of healthcare-associated infections, characterized by multidrug resistance and the emergence of global high-risk clones. However, regional genomic surveillance data remain limited. Here, we sought to characterize the population structure, transmission dynamics and resistance mechanisms of clinical K. aerogenes in Albuquerque, New Mexico. We sequenced 177 clinical isolates collected between 2021 and 2023. We also developed a novel, species-specific PopPUNK database to facilitate rapid, high-resolution typing. The New Mexico K. aerogenes population was diverse but dominated by two global pandemic lineages, ST93 (47.5%) and ST4 (7.9%), which were significantly enriched for the virulence factors yersiniabactin and colibactin. Genomic evidence for recent local transmission was rare, with only four putative transmission pairs identified. The resistome was characterized by intrinsic and adaptive mutations. Nearly all isolates possessed gyrA mutations associated with decreased fluoroquinolone susceptibility. Mutations in the AmpC regulator AmpD and the outer membrane porin Omp36 were common, particularly within the dominant ST93 lineage. These mutations have been associated with increased AmpC-mediated carbapenem resistance. Our findings underscore the critical importance of genomic surveillance to monitor the transmission and evolution of adaptive resistance.