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At least 217 records · Page 12

An adaptive lattice Boltzmann scheme for modeling two-fluid-phase flow in porous medium systems

In this paper, we formulate a multiple-relaxation-time (MRT) lattice-Boltzmann method (LBM) to simulate two-fluid-phase flow in porous medium systems. The MRT LBM is applied to simulate the displacement of a wetting fluid by a nonwetting fluid in a system corresponding to a microfluidic cell. Analysis of the simulation shows widely varying time scales for the dynamics of fluid pressures, fluid saturations, and interfacial curvatures that are typical characteristics of such systems. Displacement phenomena include Haines jumps, which are relatively short duration isolated events of rapid fluid displacement driven by capillary instability. An adaptive algorithm is advanced using a level-set method to locate interfaces and estimate their rate of advancement. Because the displacement dynamics are confined to the interfacial regions for a majority of the relaxation time, the computational effort is focused on these regions. The proposed algorithm is shown to reduce computational effort by an order of magnitude, while yielding essentially identical solutions to a conventional fully coupled approach. Finally, the challenges posed by Haines jumps are also resolved by the adaptive algorithm. Possible extensions to the advanced method are discussed.

42 ENGINEERING↗

Constellation: The autonomous control and data acquisition system for dynamic experimental setups

The operation of instruments and detectors in laboratory or beamline environments presents a complex challenge, requiring stable operation of multiple concurrent devices, often controlled by separate hardware and software solutions. These environments frequently undergo modifications, such as the inclusion of different auxiliary devices depending on the experiment or facility, adding further complexity. The successful management of such dynamic configurations demands a flexible and robust system capable of controlling data acquisition, monitoring experimental setups, enabling seamless reconfiguration, and integrating new devices with limited effort. This paper presents Constellation, a flexible and network-distributed control and data acquisition software framework tailored to laboratory and beamline environments, that addresses the limitations of existing solutions. The framework is designed with a focus on extensibility, providing a streamlined interface for instrument integration. It supports efficient system setup via network discovery mechanisms, promotes stability through autonomous operational features, and provides comprehensive documentation and supporting tools for operators and application developers such as controllers and logging interfaces. At the core of the architectural design is the autonomy of the individual components, called satellites, which can make independent decisions about their operation and communicate these decisions to other components. This paper introduces the design principles and framework architecture of Constellation, presents the available graphical user interfaces, shares insights from initial successful deployments, and provides an outlook on future developments and applications.

Autonomy↗

Ion complexation waves emerge at the curved interfaces of layered minerals

Abstract Visualizing hydrated interfaces is of widespread interest across the physical sciences and is a particularly acute need for layered minerals, whose properties are governed by the structure of the electric double layer (EDL) where mineral and solution meet. Here, we show that cryo electron microscopy and tomography enable direct imaging of the EDL at montmorillonite interfaces in monovalent electrolytes with ångstrom resolution over micron length scales. A learning-based multiple-scattering reconstruction method for cryo electron tomography reveals ions bound asymmetrically on opposite sides of curved, exfoliated layers. We observe conserved ion-density asymmetry across stacks of interacting layers in cryo electron microscopy that is associated with configurations of inner- and outer-sphere ion-water-mineral complexes that we term complexation waves. Coherent X-ray scattering confirms that complexation waves propagate at room-temperature via a competition between ion dehydration and charge interactions that are coupled across opposing sides of a layer, driving dynamic transitions between stacked and aggregated states via layer exfoliation.

36 MATERIALS SCIENCE↗

The impact of a filament eruption on nearby high-lying cool loops

The first spectroscopic observations of cool Mg II loops above the solar limb observed by NASA's Interface Region Imaging Spectrograph (IRIS) are presented. During the observation period, IRIS is pointed off-limb, allowing the observation of high-lying loops, which reach over 70 Mm in height. Low-lying cool loops were observed by the IRIS slit-jaw camera for the entire four-hour observing window. There is no evidence of a central reversal in the line profiles, and the Mg II h/k ratio is approximately two. The Mg II spectral lines show evidence of complex dynamics in the loops with Doppler velocities reaching ±40 km s{sup –1}. The complex motions seen indicate the presence of multiple threads in the loops and separate blobs. Toward the end of the observing period, a filament eruption occurs that forms the core of a coronal mass ejection. As the filament erupts, it impacts these high-lying loops, temporarily impeding these complex flows, most likely due to compression. This causes the plasma motions in the loops to become blueshifted and then redshifted. The plasma motions are seen before the loops themselves start to oscillate as they reach equilibrium following the impact. The ratio of the Mg h/k lines also increases following the impact of the filament.

79 ASTRONOMY AND ASTROPHYSICS↗

SU-D-213-03: Towards An Optimized 3D Scintillation Dosimetry Tool for Quality Assurance of Dynamic Radiotherapy Techniques

Purpose: The purpose of this work is to simulate a multi-focus plenoptic camera used as the measuring device in a real-time three-dimensional scintillation dosimeter. Simulating and optimizing this realistic optical system will bridge the technological gap between concept validation and a clinically viable tool that can provide highly efficient, accurate and precise measurements for dynamic radiotherapy techniques. Methods: The experimental prototype, previously developed for proof of concept purposes, uses an off-the-shelf multi-focus plenoptic camera. With an array of interleaved microlenses of different focal lengths, this camera records spatial and angular information of light emitted by a plastic scintillator volume. The three distinct microlens focal lengths were determined experimentally for use as baseline parameters by measuring image-to-object magnification for different distances in object space. A simulated plenoptic system was implemented using the non-sequential ray tracing software Zemax: this tool allows complete simulation of multiple optical paths by modeling interactions at interfaces such as scatter, diffraction, reflection and refraction. The active sensor was modeled based on the camera manufacturer specifications by a 2048×2048, 5 µm-pixel pitch sensor. Planar light sources, simulating the plastic scintillator volume, were employed for ray tracing simulations. Results: The microlens focal lengths were determined to be 384, 327 and 290 µm. A realistic multi-focus plenoptic system, with independently defined and optimizable specifications, was fully simulated. A f/2.9 and 54 mm-focal length Double Gauss objective was modeled as the system’s main lens. A three-focal length hexagonal microlens array of 250-µm thickness was designed, acting as an image-relay system between the main lens and sensor. Conclusion: Simulation of a fully modeled multi-focus plenoptic camera enables the decoupled optimization of the main lens and microlens specifications. This work leads the way to improving the 3D dosimeter’s achievable resolution, efficiency and build for providing a quality assurance tool fully meeting clinical needs. M.R. is financially supported by a Master’s Canada Graduate Scholarship from the NSERC. This research is also supported by the NSERC Industrial Research Chair in Optical Design.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Working with Multiple MPIs: Overcoming ABI Incompatibility

Scientific applications rely on third-party libraries, which may have multiple implementations. While sharing an application programming interface (API), many of these implementations do not have a shared application binary interface (ABI) and require recompiling. Recompiling can be a long and complex process and sometimes not even an option when the application is shipped binary only. ABI incompatibility strikes at the heart of portability, productivity, and performance by (1) impeding application execution across different HPC and Cloud systems; (2) adding developer hours rebuilding an application; and (3) not taking advantage of host-optimized libraries. This tutorial teaches attendees a portable way to address ABI incompatibility in MPI using the Wi4MPI library. Wi4MPI translates the ABI dynamically from the MPI library used to build the application to a different MPI library available at run time. With Wi4MPI, HPC practitioners can break the portability barrier imposed by ABI incompatibility, potentially increase performance, and increase user productivity. The tutorial is broken down in three components: (1) Understanding ABI compatibility in MPI; (2) Translating MPI libraries dynamically; and (3) Applying dynamic translation to key use cases in HPC, including Containers. If you use more than one MPI library or supercomputer, this tutorial is for you.

97 MATHEMATICS AND COMPUTING↗

Nanometre-resolved observation of electrochemical microenvironment formation at the nanoparticle–ligand interface

The dynamic response of surface ligands on nanoparticles (NPs) to external stimuli critically determines the functionality of NP–ligand systems. For example, in electrocatalysis the collective dissociation of ligands on NP surfaces can lead to the creation of an NP/ordered-ligand interlayer, a microenvironment that is highly active and selective for CO 2 -to-CO conversion. However, the lack of in situ characterization techniques with high spatial resolution hampers a comprehensive molecular-level understanding of the mechanism of interlayer formation. Here, in this work, we utilize in situ infrared nanospectroscopy and surface-enhanced Raman spectroscopy, unveiling an electrochemical bias-induced consecutive bond cleavage mechanism of surface ligands leading to formation of the NP/ordered-ligand interlayer. This real-time molecular insight could influence the design of confined localized fields in multiple catalytic systems. Moreover, the demonstrated capability of capturing nanometre-resolved, dynamic molecular-scale events holds promise for the advancement of using controlled local molecular behaviour to achieve desired functionalities across multiple research domains in nanoscience.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Adaptive tau-leaping methods for microscopic-lattice kinetic Monte Carlo simulations

Traditional Kinetic Monte Carlo (KMC) approaches, rooted in Gillespie’s stochastic simulation algorithm, become computationally demanding in systems with a large range of timescales. The goal of this work is to propose and study new adaptive lattice-KMC time integration strategies for spatially non-uniform systems. To that end, two novel adaptive tau-leaping methods and their corresponding time integration strategies are developed based on the idea of the “n-fold” direct KMC method. These strategies allow for the simultaneous execution of multiple reactions, advancing time by adaptively selected coarse increments. We present numerical experiments comparing the proposed methods with existing approaches in a catalytic surface kinetics application involving ammonia decomposition.

Bimolecular reactions↗

Analysis of Binding Site Hot Spots on the Surface of Ras GTPase

We have recently discovered an allosteric switch in Ras, bringing an additional level of complexity to this GTPase whose mutants are involved in nearly 30% of cancers. Upon activation of the allosteric switch, there is a shift in helix 3/loop 7 associated with a disorder to order transition in the active site. Here, we use a combination of multiple solvent crystal structures and computational solvent mapping (FTMap) to determine binding site hot spots in the 'off' and 'on' allosteric states of the GTP-bound form of H-Ras. Thirteen sites are revealed, expanding possible target sites for ligand binding well beyond the active site. Comparison of FTMaps for the H and K isoforms reveals essentially identical hot spots. Furthermore, using NMR measurements of spin relaxation, we determined that K-Ras exhibits global conformational dynamics very similar to those we previously reported for H-Ras. We thus hypothesize that the global conformational rearrangement serves as a mechanism for allosteric coupling between the effector interface and remote hot spots in all Ras isoforms. At least with respect to the binding sites involving the G domain, H-Ras is an excellent model for K-Ras and probably N-Ras as well. Ras has so far been elusive as a target for drug design. The present work identifies various unexplored hot spots throughout the entire surface of Ras, extending the focus from the disordered active site to well-ordered locations that should be easier to target.

59 BASIC BIOLOGICAL SCIENCES↗

A non-intrusive parallel-in-time adjoint solver with the XBraid library

In this paper, an adjoint solver for the multigrid-in-time software library XBraid is presented. XBraid provides a non-intrusive approach for simulating unsteady dynamics on multiple processors while parallelizing not only in space but also in the time domain (XBraid: Parallel multigrid in time, http://llnl.gov/casc/xbraid). It applies an iterative multigrid reduction in time algorithm to existing spatially parallel classical time propagators and computes the unsteady solution parallel in time. Techniques from Automatic Differentiation are used to develop a consistent discrete adjoint solver which provides sensitivity information of output quantities with respect to design parameter changes. The adjoint code runs backwards through the primal XBraid actions and accumulates gradient information parallel in time. It is highly non-intrusive as existing adjoint time propagators can easily be integrated through the adjoint interface. The adjoint code is validated on advection-dominated flow with periodic upstream boundary condition. We report it provides similar strong scaling results as the primal XBraid solver and offers great potential for speeding up the overall computational costs for sensitivity analysis using multiple processors.

97 MATHEMATICS AND COMPUTING↗

Challenges in studying water fluxes within the soil-plant-atmosphere continuum: A tracer-based perspective on pathways to progress

Tracing and quantifying water fluxes in the hydrological cycle is crucial for understanding the current state of ecohydrological systems and their vulnerability to environmental change. Especially the interface between ecosystems and the atmosphere that is strongly mediated by plants is important to meaningfully describe ecohydrological system functioning. Many of the dynamic interactions generated by water fluxes between soil, plant and the atmosphere are not well understood, which is partly due to a lack of interdisciplinary research. This opinion paper reflects the outcome of a discussion among hydrologists, plant ecophysiologists and soil scientists on open questions and new opportunities for collaborative research on the topic "water fluxes in the soil-plant-atmosphere continuum" especially focusing on environmental and artificial tracers. We emphasize the need for a multi-scale experimental approach, where a hypothesis is tested at multiple spatial scales and under diverse environmental conditions to better describe the small-scale processes (i.e., causes) that lead to large-scale patterns of ecosystem functioning (i.e., consequences). Novel in-situ, high-frequency measurement techniques offer the opportunity to sample data at a high spatial and temporal resolution needed to understand the underlying processes. Here we advocate for a combination of long-term natural abundance measurements and event-based approaches. Multiple environmental and artificial tracers, such as stable isotopes, and a suite of experimental and analytical approaches should be combined to complement information gained by different methods. Virtual experiments using process-based models should be used to inform sampling campaigns and field experiments, e.g., to improve experimental designs and to simulate experimental outcomes. On the other hand, experimental data are a pre-requisite to improve our currently incomplete models. Interdisciplinary collaboration will help to overcome research gaps that overlap across different earth system science fields and help to generate a more holistic view of water fluxes between soil, plant and atmosphere in diverse ecosystems.

54 ENVIRONMENTAL SCIENCES↗

Temporal Sampling of Enzymes from Live Cells by Localized Electroporation and Quantification of Activity by SAMDI Mass Spectrometry

Abstract Measuring changes in enzymatic activity over time from small numbers of cells remains a significant technical challenge. In this work, a method for sampling the cytoplasm of cells is introduced to extract enzymes and measure their activity at multiple time points. A microfluidic device, termed the live cell analysis device (LCAD), is designed, where cells are cultured in microwell arrays fabricated on polymer membranes containing nanochannels. Localized electroporation of the cells opens transient pores in the cell membrane at the interface with the nanochannels, enabling extraction of enzymes into nanoliter‐volume chambers. In the extraction chambers, the enzymes modify immobilized substrates, and their activity is quantified by self‐assembled monolayers for matrix‐assisted laser desorption/ionization (SAMDI) mass spectrometry. By employing the LCAD‐SAMDI platform, protein delivery into cells is demonstrated. Next, it is shown that enzymes can be extracted, and their activity measured without a loss in viability. Lastly, cells are sampled at multiple time points to study changes in phosphatase activity in response to oxidation by hydrogen peroxide. With this unique sampling device and label‐free assay format, the LCAD with SAMDI enables a powerful new method for monitoring the dynamics of cellular activity from small populations of cells.

Mukherjee, Prithvijit↗

Image method for induced surface charge from many-body system of dielectric spheres

Charged dielectric spheres embedded in a dielectric medium provide the simplest model for many-body systems of polarizable ions and charged colloidal particles. We provide a multiple scattering formulation for the total electrostatic energy for such systems and demonstrate that the polarization energy can be rapidly evaluated by an image method that generalizes the image methods for conducting spheres. Furthermore, individual contributions to the total electrostatic energy are ordered according to the number of polarized surfaces involved, and each additional surface polarization reduces the energy by a factor of $(a/R)^3ϵ$, where $a$ is the sphere radius, $R$ the average inter-sphere separation, and $ϵ$ the relevant dielectric mismatch at the interface. Explicit expressions are provided for both the energy and the forces acting on individual spheres, which can be readily implemented in Monte Carlo and molecular dynamics simulations of polarizable charged spheres, thereby avoiding costly computational techniques that introduce a surface charge distribution that requires numerical solution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

HOMMEXX 1.0: a performance-portable atmospheric dynamical core for the Energy Exascale Earth System Model

Abstract. We present an architecture-portable and performant implementation of the atmospheric dynamical core (High-Order Methods Modeling Environment, HOMME) of the Energy Exascale Earth System Model (E3SM). The original Fortran implementation is highly performant and scalable on conventional architectures using the Message Passing Interface(MPI) and Open MultiProcessor (OpenMP) programming models.We rewrite the model in C++ and use the Kokkos library to express on-node parallelism in a largely architecture-independent implementation. Kokkos provides an abstraction of a compute node or device,layout-polymorphic multidimensional arrays, and parallel execution constructs. The new implementation achieves the same or better performance on conventional multicore computers and is portable to GPUs. We present performance data for the original and new implementations on multiple platforms, on up to 5400 compute nodes, and study several aspects of the single- and multi-node performance characteristics of the new implementation on conventional CPU (e.g., Intel Xeon), many core CPU (e.g., Intel Xeon Phi Knights Landing),and Nvidia V100 GPU.

58 GEOSCIENCES↗

On the Suitability of MPI as a PGAS Runtime

Partitioned Global Address Space (PGAS) models are emerging as a popular alternative to MPI models for designing scalable applications. At the same time, MPI remains a ubiquitous communication subsystem due to its standardization, high performance, and availability on leading platforms. In this paper, we explore the suitability of using MPI as a scalable PGAS communication subsystem. We focus on the Remote Memory Access (RMA) communication in PGAS models which typically includes {\em get, put,} and {\em atomic memory operations}. We perform an in-depth exploration of design alternatives based on MPI. These alternatives include using a semantically-matching interface such as MPI-RMA, as well as not-so-intuitive interfaces such as MPI two-sided with a combination of multi-threading and dynamic process management. With an in-depth exploration of these alternatives and their shortcomings, we propose a novel design which is facilitated by the data-centric view in PGAS models. This design leverages a combination of highly tuned MPI two-sided semantics and an automatic, user-transparent split of MPI communicators to provide asynchronous progress. We implement the asynchronous progress ranks approach and other approaches within the Communication Runtime for Exascale which is a communication subsystem for Global Arrays. Our performance evaluation spans pure communication benchmarks, graph community detection and sparse matrix-vector multiplication kernels, and a computational chemistry application. The utility of our proposed PR-based approach is demonstrated by a 2.17x speed-up on 1008 processors over the other MPI-based designs.

Computational modeling↗

Refactoring the elastic–viscous–plastic solver from the sea ice model CICE v6.5.1 for improved performance

This study focuses on the performance of the elastic–viscous–plastic (EVP) dynamical solver within the sea ice model, CICE v6.5.1. The study has been conducted in two steps. First, the standard EVP solver was extracted from CICE for experiments with refactored versions, which are used for performance testing. Second, one refactored version was integrated and tested in the full CICE model to demonstrate that the new algorithms do not significantly impact the physical results. The study reveals two dominant bottlenecks, namely (1) the number of Message Parsing Interface (MPI) and Open Multi-Processing (OpenMP) synchronization points required for halo exchanges during each time step combined with the irregular domain of active sea ice points and (2) the lack of single-instruction, multiple-data (SIMD) code generation. The standard EVP solver has been refactored based on two generic patterns. The first pattern exposes how general finite differences on masked multi-dimensional arrays can be expressed in order to produce significantly better code generation by changing the memory access pattern from random access to direct access. The second pattern takes an alternative approach to handle static grid properties. The measured single-core performance improvement is more than a factor of 5 compared to the standard implementation. The refactored implementation of strong scales on the Intel® Xeon® Scalable Processors series node until the available bandwidth of the node is used. For the Intel® Xeon® CPU Max series, there is sufficient bandwidth to allow the strong scaling to continue for all the cores on the node, resulting in a single-node improvement factor of 35 over the standard implementation. This study also demonstrates improved performance on GPU processors.

58 GEOSCIENCES↗

Ensembles of Metastable States Govern Heterogeneous Catalysis on Dynamic Interfaces

Heterogeneous catalysis is at the heart of chemical industry. Being able to tune and design efficient catalysts for processes of interest is of an utmost importance, and for this, the molecular-level understanding of heterogeneous catalysts is the first step, and indeed a prime focus of the modern catalysis research. For a long time, a single most thermodynamically stable structure of the catalytic interface attained in reaction conditions had been envisioned as the reactive phase. However, some catalytic interfaces continue to undergo structural dynamics in the steady state, triggered by high temperatures, pressures, and binding and changing reagents. Among particularly dynamic interfaces are such widely-used catalysts as crystalline and amorphous surfaced supporting (sub-)nano metallic clusters. Recently, it became clear that this dynamic fluxionality causes the supported clusters to populate many distinct structural and stoichiometric states in catalytic conditions. Hence, the catalytic interface should be viewed as an evolving statistical ensemble of many (not one) structures. As such, every member in the ensemble contributes to the properties of the catalyst differently, and in proportion to its probability to be populated. This new notion flips the established paradigm and calls for new theory, modeling approaches, operando measurements, and updated design strategies. The statistical ensemble nature of surface-supported sub-nano cluster catalysts can be exemplified by oxide-supported and adsorbate-covered Pt, Pd, Cu, CuPd clusters, catalytic toward oxidative and non-oxidative dehydrogenation. They have access to a variety of 3D and quasi-2D shapes. The compositions of their thermal ensembles are dependent on the cluster size, leading to size-specific catalytic activities and the famous “every atom counts” phenomenon. The support and adsorbates affect catalyst structures, and state of the reacting species causes the ensemble to change in every reaction intermediate. The most stable member of the ensemble dominates the thermodynamic properties of the corresponding intermediate, whereas the kinetics can be determined by more active but less populated metastable catalyst states, and that suggests that many earlier studies might have overlooked the actual active sites. Both effects depend on the relative time-scales of catalyst restructuring and reaction dynamics. The catalyst may routinely operate off-equilibrium. Ensemble phenomena lead to surprising exceptions from established rules of catalysis, such as scaling relations, and Arrhenius behavior. Catalyst deactivation is also an ensemble property, and its extent of mitigation can be predicted through the new paradigm. These findings were enabled by advances in theory, such as global optimization and subsequent utilization of multiple local minima, and pathways sampling, as well as operando catalyst characterization. The fact that the per-site and per-species resolution is needed for the description and predicting of catalyst properties gives theory the central role in catalysis research, as most experiments provide ensemble-average information and cannot detect the crucial minority species that may be responsible for the catalytic activity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Scalable simulation of coupled adsorption and transport of methane in confined complex porous media with density preconditioning

The growing significance of shales and tight formations in the transition to less carbon-intensive and clean energy drives the research endeavor to understand the physics of gas flow within these systems. However, shales are composed of massively heterogeneous physical and chemical features. Most nano-sized pores connect to millimeter-scale fractures, leading to multiscale transport. These nano-scale pore throats demonstrate non-classical flow behavior, such as non-negligible slip velocities and adsorbed gas layers at the boundary. As a result, classical computational fluid dynamics models do not capture the physics. In this work, we develop a coupling scheme for the multiple-relaxation-time (MRT) lattice Boltzmann (LB) method that integrates the Peng-Robinson equation of state into a pseudo-potential interaction model to capture the physics of methane flow in irregular networks of channels that represent nano-scale porous media. We use atomistic simulations to calibrate and validate our model in slit nano-channels. We propose a preconditioning scheme to initialize the coupled transport and adsorption simulation of methane in complex porous media. The results of this implementation of LB agree with Direct Simulation Monte Carlo (DSMC) and Molecular Dynamics (MD) simulations. We then scale up the LB implementation through vectorization and indirect addressing. We parallelize it using Message Passing Interface (MPI) and OpenMP frameworks to simulate transport and adsorption in complex media with a million lattices. Additionally, we analyze the differences between coupled and transport-only simulations in two case studies and show that considering phase behavior, i.e., adsorption, can significantly change the flow behavior. This work constitutes an important step towards bridging the gap between molecular flow and system-scale behavior of complex disordered porous media.

42 ENGINEERING↗