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At least 37 records · Page 2

Transitioning from File-Based HPC Workflows to Streaming Data Pipelines with openPMD and ADIOS2

This paper aims to create a transition path from file-based IO to streaming-based workflows for scientific applications in an HPC environment. By using the openPMP-api, traditional workflows limited by filesystem bottlenecks can be overcome and flexibly extended for in situ analysis. The openPMD-api is a library for the description of scientific data according to the Open Standard for Particle-Mesh Data (openPMD). Its approach towards recent challenges posed by hardware heterogeneity lies in the decoupling of data description in domain sciences, such as plasma physics simulations, from concrete implementations in hardware and IO. The streaming backend is provided by the ADIOS2 framework, developed at Oak Ridge National Laboratory. This paper surveys two openPMD-based loosely-coupled setups to demonstrate flexible applicability and to evaluate performance. In loose coupling, as opposed to tight coupling, two (or more) applications are executed separately, e.g. in individual MPI contexts, yet cooperate by exchanging data. This way, a streaming-based workflow allows for standalone codes instead of tightly-coupled plugins, using a unified streaming-aware API and leveraging high-speed communication infrastructure available in modern compute clusters for massive data exchange. We determine new challenges in resource allocation and in the need of strategies for a flexible data distribution, demonstrating their influence on efficiency and scaling on the Summit compute system. The presented setups show the potential for a more flexible use of compute resources brought by streaming IO as well as the ability to increase throughput by avoiding filesystem bottlenecks.

Poeschel, Franz↗

Tribute to Lawrence R. Pratt

Lawrence Pratt’s career following completion of his Ph.D. at the University of Illinois Urbana Champaign has taken him from Harvard University, to the University of California, Berkeley, and Los Alamos National Laboratory. Most recently, he joined the faculty of the Department of Chemical and Biomolecular Engineering at Tulane University in 2008. Over his career Lawrence has been a leader in theoretical physical chemistry, making influential contributions to a number of areas including the theory of the hydrophobic effect, the development of transition path sampling, contributions to orbital free density functional theory, and the theory of liquids and solutions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Giant electric field-induced second harmonic generation in polar skyrmions

Electric field-induced second harmonic generation allows electrically controlling nonlinear light-matter interactions crucial for emerging integrated photonics applications. Despite its wide presence in materials, the figures-of-merit of electric field-induced second harmonic generation are yet to be elevated to enable novel device functionalities. Here, we show that the polar skyrmions, a topological phase spontaneously formed in PbTiO3/SrTiO3 ferroelectric superlattices, exhibit a high comprehensive electric field-induced second harmonic generation performance. The second-order nonlinear susceptibility and modulation depth, measured under non-resonant 800 nm excitation, reach ~54.2 pm V −1 and ~664% V −1 , respectively, and high response bandwidth (higher than 10 MHz), wide operating temperature range (up to ~400 K) and good fatigue resistance (>10 10 cycles) are also demonstrated. Through combined in-situ experiments and phase-field simulations, we establish the microscopic links between the exotic polarization configuration and field-induced transition paths of the skyrmions and their electric field-induced second harmonic generation response. Our study not only presents a highly competitive thin-film material ready for constructing on-chip devices, but opens up new avenues of utilizing topological polar structures in the fields of photonics and optoelectronics.

Nonlinear optics↗

The reaction mechanism of the Ideonella sakaiensis PETase enzyme

Abstract Polyethylene terephthalate (PET), the most abundantly produced polyester plastic, can be depolymerized by the Ideonella sakaiensis PETase enzyme. Based on multiple PETase crystal structures, the reaction has been proposed to proceed via a two-step serine hydrolase mechanism mediated by a serine-histidine-aspartate catalytic triad. To elucidate the multi-step PETase catalytic mechanism, we use transition path sampling and likelihood maximization to identify optimal reaction coordinates for the PETase enzyme. We predict that deacylation is likely rate-limiting, and the reaction coordinates for both steps include elements describing nucleophilic attack, ester bond cleavage, and the “moving-histidine” mechanism. We find that the flexibility of Trp185 promotes the reaction, providing an explanation for decreased activity observed in mutations that restrict Trp185 motion. Overall, this study uses unbiased computational approaches to reveal the detailed reaction mechanism necessary for further engineering of an important class of enzymes for plastics bioconversion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Solvent reaction coordinate for an S N 2 reaction

We study the prototypical S N 2 reaction Cl – + CH 3 Cl → CH 3 Cl + Cl – in water using QM/MM computer simulations with transition path sampling and inertial likelihood maximization. We have identified a new solvent coordinate that improves upon the original atom-exchange coordinate used in the classic analysis by Chandrasekhar, Smith, and Jorgensen. The new solvent coordinate quantifies instantaneous solvent induced polarization relative to equilibrium charge density at each point along the reaction pathway. In this paper, we will present free energy surfaces, transmission coefficients, and committor tests associated with this collective coordinate.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Field-driven ion pairing dynamics in concentrated electrolytes

Here, we investigate ion pairing dynamics in electrolytes driven far from equilibrium using molecular simulations and nonequilibrium rate theory. Focusing on 0.5M LiPF 6 in water and acetonitrile under uniform electric fields, we compute transition path theory observables, including reactive fluxes and mean first-passage times of ion pairing. Moreover, we introduce a dynamical proxy of free-ion population, where its field-induced change is strongly correlated with the nonlinear enhancement of conductivity, yielding an increase of 40% at 50 mV/Å in acetonitrile, compared to that of less than 10% in aqueous electrolytes. Further kinetic analysis elucidates that Onsager’s classical theory substantially overestimates field-induced enhancement of ion pair dissociation in molecular electrolytes. This discrepancy arises from solvent-mediated dynamical pathways and field-induced dielectric decrement that suppress ion pair dissociation within explicit solvents, highlighting that a faithful description of molecular details is essential. Our results provide a molecular interpretation of nonlinear electrolyte transport beyond continuum theories and establish a general framework for quantifying nonequilibrium reaction kinetics in condensed phase systems.

Moon, Seokjin [University of California, Berkeley,↗

The incommensurately modulated structures of low-temperature labradorite feldspars: a single-crystal X-ray and neutron diffraction study

Labradorite feldspars of the plagioclase solid solution series have been known for their complicated subsolidus phase relations and enigmatic incommensurately modulated structures. Characterized by the irrationally indexed e -reflections in the diffraction pattern, e -labradorite shows the largest variation in the incommensurate ordering states among the e -plagioclase structures. The strongly ordered low-temperature e -labradorite is one of the last missing pieces of the e -plagioclase puzzle. Nine plutonic and metamorphic labradorite feldspar samples from Canada, Ukraine, Minnesota (USA), Tanzania and Greenland with compositions ranging from An 52.5 to An 68 were studied with single-crystal X-ray diffraction. Two crystals from Labrador, Canada, and Duluth, MN, USA, with wide enough twin lamellae were analyzed with single-crystal neutron diffraction. The incommensurately modulated structures of e -plagioclase are refined for the first time with neutron diffraction data, which confirmed that the T—O distance modulation in the low-temperature e -plagioclase results from the Al–Si ordering in the framework. Detailed configurations of the M site are also observed in the structures refined from neutron diffraction data, which were not possible to see with X-ray diffraction data. The relation between the q -vectors and the mole% An composition is revealed for the entire compositional range of e -plagioclase, from An 25 to An 75 . The previously proposed two-trend relation depending on the cooling rate and phase transition path is confirmed. A new classification of e -plagioclase ( e α , e β and e γ ) is proposed based on the q -vector of the structure, which makes it an independent character from the presence/absence of density modulation. New parameters are proposed to quantify the ordering states of these complicated aperiodic structures of e -plagioclases, such as the difference between $\langle$T 1 o—O$\rangle$ and $\langle$T 1 m—O$\rangle$ at phase t = 0.2 or the normalized intensity of the (071\bar 1) reflection.

36 MATERIALS SCIENCE↗

Association of Cl with C 2 H 2 by unified variable-reaction-coordinate and reaction-path variational transition-state theory

Significance A key issue in chemical kinetics is advancing the theoretical framework to handle reactions beyond the domain of textbook transition-state theory by including––for example––anharmonicity, barrierless transition states, transition states in series, and the effect of conformational flexibility on equilibrium constants. Other key issues are validating affordable electronic structure methods for direct dynamics and the direct calculation of high-pressure limiting rate constants, which are often obtainable experimentally only by extrapolation. The present article addresses all these issues for a prototype radical–molecule association reaction and thereby demonstrates how to combine improved theoretical methods to provide rate constants in cases where experimental data are uncertain or missing.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Integrating a Water Tracer Model Into WRF‐Hydro for Characterizing the Effect of Lateral Flow in Hydrologic Simulations

Abstract Most current land models approximate terrestrial hydrological processes as one‐dimensional vertical flow, neglecting lateral water movement from ridges to valleys. Such lateral flow is fundamental at catchment scales and becomes crucial for finer‐scale land models. To test the effect of incorporating lateral flow toward three‐dimensional representations of hydrological processes in the next generation land models, we integrate a water tracer model into the WRF‐Hydro framework to track water movement from precipitation to discharge and evapotranspiration. This hydrologic‐tracer integrated system allows us to identify the key mechanisms by which lateral flow affects the flow paths and transit times in WRF‐Hydro. By comparing modeling experiments with and without lateral routing in two contrasting catchments, we determine the impacts of lateral flow on the transit times of precipitation event‐water. Results show that with limited hydrologic connectivity, lateral flow extends the transit times by reducing (increasing) event‐water drainage loss (accumulation) in ridges (valleys) and allowing reinfiltration of infiltration‐excess flow, which is missing in most land models. On the contrary with high hydrologic connectivity, lateral flow can effectively accelerate the water release to streams and reduce the transit time. However, the transit times are substantially underestimated by the model compared with isotope‐derived estimates, indicating model limitations in representing flow paths and transit times. This study provides some insights on the fundamental differences in terrestrial hydrology simulated by land models with and without lateral flow representation.

54 ENVIRONMENTAL SCIENCES↗

Thermodynamic signatures of an antiferromagnetic quantum critical point inside a superconducting dome

Recent experiments in unconventional superconductors, and in particular iron-based materials, have reported evidence of an antiferromagnetic quantum critical point (AFM-QCP) emerging inside the superconducting dome of the phase diagram. Fluctuations associated with such an AFM-QCP are expected to promote unusual temperature dependencies of thermodynamic quantities. Here, we compute the T dependence of the specific heat C(T) deep inside a fully gapped s +– superconducting state as the AFM-QCP is approached. We find that at the AFM-QCP, the specific heat C(T) vanishes quadratically with temperature, as opposed to the typical exponential suppression seen in fully gapped BCS superconductors. This robust result is due to a nonanalytic contribution to the free energy arising from the general form of the bosonic (AFM) propagator in the SC state. Away from the AFM-QCP, as temperature is lowered, C(T) shows a crossover from a T2 behavior to an exponential behavior, with the crossover temperature scale set by the value of the superconducting gap and the distance to the QCP. As a result, we argue that these features in the specific heat can be used to unambiguously determine the existence of AFM-QCPs inside the superconducting domes of iron-based and other fully gapped unconventional superconductors.

36 MATERIALS SCIENCE↗

Mechanistic study of a CO-free pathway in the methanol oxidation reaction over oxygen vacancies in NiOOH

The methanol oxidation reaction is a key reaction in direct methanol fuel cells. Prior research indicates that if oxygen vacancies in NiOOH serve as the active sites, the methanol oxidation mainly proceeds through the formate-involving pathway, which is a CO-free pathway, distinct from the conventional path over transition metal catalysts, though the fundamental reason for this suppressed CO formation is unclear. Herein, we report density functional theory calculations, through which we uncover the underlying reasons for this alternate path of methanol oxidation over the oxygen vacancies in NiOOH. We find that the existence of oxygen vacancies in NiOOH affects the adsorption configuration of adsorbates and that the interfacial charge transfer is minimal for CHO and CO intermediates. In addition, CHO, a key intermediate to form CO, adsorbs at the oxygen vacancy through the oxygen atom, leading to low stability due to the incomplete valence saturation of the carbon atom. This weak electronic interaction and instability effectively inhibit CHO formation and, consequently, CO formation. These insights provide valuable guidance for the development of efficient and CO-tolerant catalysts for methanol oxidation.

Ho, Thy [University of Oklahoma, Norman, OK (Unite↗

Dynamic strength of iron under pressure-temperature conditions of Earth’s inner core

Iron (Fe) is a primary constituent of terrestrial planetary cores, yet its rheological properties under extreme conditions remain uncertain. Here we present direct measurements of Fe strength at 310-430 GPa pressures and 3700-5800 K temperatures, obtained using Rayleigh-Taylor (RT) instability experiments at the National Ignition Facility. Single-crystal α-Fe samples with [001] and [111] orientations are shock-ramp compressed past the α-ε transition along paths approaching Earth’s inner core conditions. We find that ε-Fe derived from [001] α-Fe is consistently stronger (11-20 GPa) than that from [111] α-Fe (8-18 GPa), contrary to the trend at ambient conditions. Large-scale molecular dynamics simulations reproduce this atypical strength anisotropy and attribute it to microstructural evolution during the phase transition and subsequent ε-phase plasticity. Ripple growth analysis further constrains viscosities of 100-170 Pa·s under the driven conditions. Our results provide experimental benchmarks for Fe rheology at inner-core conditions, with implications for seismic anisotropy and the geodynamo.

Condensed-matter physics↗

Redesigning large-scale multimodal transit networks with shared autonomous mobility services

Here, this study addresses a large-scale multimodal transit network design problem, with Shared Autonomous Mobility Services (SAMS) as both transit feeders and an origin-to-destination mode. The framework captures spatial demand and modal characteristics, considers intermodal transfers and express services, determines transit infrastructure investment and path flows, and generates transit routes. A system-optimal multimodal transit network is designed with minimum total door-to-door generalized costs of users and operators, satisfying transit origin-destination demand within a pre-set infrastructure budget. Firstly, the geography, demand, and modes in each zone are characterized with continuous approximation. The decisions of network link investment and multimodal path flows in zonal connection optimization are formulated as a minimum-cost multi-commodity network flow (MCNF) problem and solved efficiently with a mixed-integer linear programming (MILP) solver. Subsequently, the route generation problem is solved by expanding the MCNF formulation to minimize intramodal transfers. The model is illustrated through a set of experiments with the Chicago network comprised of 50 zones and seven modes, under three scenarios. The computational results present savings in traveler journey time and operator cost demonstrating the potential benefits of collaboration between multimodal transit systems and SAMS.

Autonomous vehicles↗

Toward Drilling the Perfect Geothermal Well: An International Research Coordination Network for Geothermal Drilling Optimization Supported by Deep Machine Learning and Cloud Based Data Aggregation

The EDGE project, supported by the U.S. Department of Energy Geothermal Technologies Office under award DE-EE0008793, established a data-driven framework for improving the efficiency, cost-effectiveness, and reliability of geothermal well drilling. The project focused on developing scalable data infrastructure, advanced machine learning and probabilistic models, and integrated analytics tools to support continuous drilling optimization. A central objective was to reduce geothermal drilling costs by up to seventy percent while minimizing the risk of well failure through predictive diagnostics and adaptive planning. Over the project period, a comprehensive data repository was designed and deployed, incorporating records from over one hundred geothermal wells across varied geological settings. This repository supported both structured and unstructured data and adhered to FAIR data principles, enabling provenance tracking, quality control, and standardized metadata. The project introduced automated ingestion pipelines and a cloud-hosted platform that facilitated access to raw, processed, and derived datasets. This infrastructure served as the foundation for model development and analysis. Machine learning workflows were developed to predict key drilling metrics including rate of penetration, non-productive time, and total drilling costs. Self-organizing maps and dimensionality reduction methods were used to uncover operational patterns and outliers, while supervised learning algorithms such as random forests and deep neural networks were applied to forecast performance outcomes. The models were validated on heterogeneous datasets from both U.S. and Icelandic fields, demonstrating variable but significant predictive accuracy. The results indicated that finer temporal resolution, inclusion of lithological data, and consistency in operational annotations could substantially improve model performance. The project also implemented process mining techniques to reconstruct state-transition models from drilling event logs. These models enabled the identification of deviations from optimal workflows and provided insights into recurring failure modes. Analysis of non-productive time highlighted the impact of equipment failures, geological challenges, and human factors, offering opportunities for targeted mitigation strategies. The EDGE Dashboard was developed as a web-based expert system integrating data visualization, model outputs, and user-driven queries. It provided an accessible interface for operators to explore historical data, evaluate predicted outcomes, and compare drilling scenarios. Initial feedback from project partners suggested that the dashboard could serve as a foundation for more advanced advisory and optimization tools. Overall, the EDGE project demonstrated the feasibility and value of applying modern data science techniques to geothermal drilling. It delivered a set of interoperable tools and models that can support more efficient, lower-risk well development. The findings point toward a viable path for transitioning from advisory analytics to semi-autonomous drilling systems, contingent on continued collaboration, expanded datasets, and field validation. The project results have immediate relevance for drilling operations, data management practices, and future geothermal R&D efforts aimed at achieving reliable, cost-competitive geothermal energy at scale.

15 GEOTHERMAL ENERGY↗

Sustained Oxygen Spectral Gaps and Their Dynamic Evolution in the Inner Magnetosphere

Van Allen Probes observations of ion spectra often show a sustained gap within a very narrow energy range throughout the full orbit. To understand their formation mechanism, we statistically investigate the characteristics of the narrow gaps for oxygen ions and find that they are most frequently observed near the noon sector with a peak occurrence rate of over 30%. The magnetic moment (μ) of the oxygen ions in the gap shows a strong dependence on magnetic local time (MLT), with higher and lower μ values in the morning and afternoon sectors, respectively. Moreover, we find through superposed epoch analysis that the gap formation also depends on geomagnetic conditions. Those gaps formed at lower magnetic moments (μ < 3,000 keV/G) are associated with stable convection electric fields, which enable magnetospheric ions to follow a steady drift pattern that facilitates the gap formation by corotational drift resonance. On the other hand, gaps with higher μ values are statistically preceded by a gradual increase of geomagnetic activity. Here, we suggest that ions within the gap were originally located inside the Alfven layer following closed drift paths, before they were transitioned into open drift paths as the convection electric field was enhanced. The sunward drift of these ions, with very low fluxes, forms a drainage void in the dayside magnetosphere manifested as the sustained gap in the oxygen spectrum. This scenario is supported by particle-tracing simulations, which reproduce most of the observed characteristics and therefore provide new insights into inner magnetospheric dynamics.

79 ASTRONOMY AND ASTROPHYSICS↗

Designing polar textures with ultrafast neuromorphic features from atomistic simulations

This review summarizes recent works, all using a specific atomistic approach, that predict and explain the occurrence of key features for neuromorphic computing in three archetypical dipolar materials, when they are subject to THz excitations. The main ideas behind such atomistic approach are provided, and illustration of model relaxor ferroelectrics, antiferroelectrics, and normal ferroelectrics are given, highlighting the important potential of polar materials as candidates for neuromorphic computing. Some peculiar emphases are made in this Review, such as the connection between neuromorphic features and percolation theory, local minima in energy path, topological transitions and/or anharmonic oscillator model, depending on the material under investigation. By considering three different and main polar material families, this work provides a complete and innovative toolbox for designing polar-based neuromorphic systems.

THz pulses↗

Quantum-Accurate Multiscale Modeling of Shock Hugoniots, Ramp Compression Paths, Structural and Magnetic Phase Transitions, and Transport Properties in Highly Compressed Metals

Fully characterizing high energy density (HED) phenomena using pulsed power facilities (Z machine) and coherent light sources is possible only with complementary numerical modeling for design, diagnostic development, and data interpretation. The exercise of creating numerical tests, that match experimental conditions, builds critical insight that is crucial for the development of a strong fundamental understanding of the physics behind HED phenomena and for the design of next generation pulsed power facilities. The persistence of electron correlation in HED materials arising from Coulomb interactions and the Pauli exclusion principle is one of the greatest challenges for accurate numerical modeling and has hitherto impeded our ability to model HED phenomena across multiple length and time scales at sufficient accuracy. An exemplar is a ferromagnetic material like iron, while familiar and widely used, we lack a simulation capability to characterize the interplay of structure and magnetic effects that govern material strength, kinetics of phase transitions and other transport properties. Herein we construct and demonstrate the Molecular-Spin Dynamics (MSD) simulation capability for iron from ambient to earth core conditions, all software advances are open source and presently available for broad usage. These methods are multi-scale in nature, direct comparisons between high fidelity density functional theory (DFT) and linear-scaling MSD simulations is done throughout this work, with advancements made to MSD allowing for electronic structure changes being reflected in classical dynamics. Main takeaways for the project include insight into the role of magnetic spins on mechanical properties and thermal conductivity, development of accurate interatomic potentials paired with spin Hamiltonians, and characterization of the high pressure melt boundary that is of critical importance to planetary modeling efforts.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗