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At least 1,135 records · Page 63

Compute as Fast as the Engineers Can Think! ULTRAFAST COMPUTING TEAM FINAL REPORT

This report documents findings and recommendations by the Ultrafast Computing Team (UCT). In the period 10-12/98, UCT reviewed design case scenarios for a supersonic transport and a reusable launch vehicle to derive computing requirements necessary for support of a design process with efficiency so radically improved that human thought rather than the computer paces the process. Assessment of the present computing capability against the above requirements indicated a need for further improvement in computing speed by several orders of magnitude to reduce time to solution from tens of hours to seconds in major applications. Evaluation of the trends in computer technology revealed a potential to attain the postulated improvement by further increases of single processor performance combined with massively parallel processing in a heterogeneous environment. However, utilization of massively parallel processing to its full capability will require redevelopment of the engineering analysis and optimization methods, including invention of new paradigms. To that end UCT recommends initiation of a new activity at LaRC called Computational Engineering for development of new methods and tools geared to the new computer architectures in disciplines, their coordination, and validation and benefit demonstration through applications.

Biedron, R. T.↗

Higher-Order Theory for Functionally Graded Materials

Functionally graded materials (FGM's) are a new generation of engineered materials wherein the microstructural details are spatially varied through nonuniform distribution of the reinforcement phase(s). Engineers accomplish this by using reinforcements with different properties, sizes, and shapes, as well as by interchanging the roles of the reinforcement and matrix phases in a continuous manner (ref. 1). The result is a microstructure that produces continuously or discretely changing thermal and mechanical properties at the macroscopic or continuum scale. This new concept of engineering the material's microstructure marks the beginning of a revolution both in the materials science and mechanics of materials areas since it allows one, for the first time, to fully integrate the material and structural considerations into the final design of structural components. Functionally graded materials are ideal candidates for applications involving severe thermal gradients, ranging from thermal structures in advanced aircraft and aerospace engines to computer circuit boards. Owing to the many variables that control the design of functionally graded microstructures, full exploitation of the FGM's potential requires the development of appropriate modeling strategies for their response to combined thermomechanical loads. Previously, most computational strategies for the response of FGM's did not explicitly couple the material's heterogeneous microstructure with the structural global analysis. Rather, local effective or macroscopic properties at a given point within the FGM were first obtained through homogenization based on a chosen micromechanics scheme and then subsequently used in a global thermomechanical analysis.

Aboudi, J.↗

BGK-MD, Version 1.0

The software implements a heterogeneous multiscale method (HMM), which involves solving a classical molecular dynamics (MD) problem and then computes the entropy production in order to compute the relaxation times towards equilibrium for use in a Bhatnagar-Gross-Krook (BGK) solver.

Haack, Jeffrey↗

The Role of Mathematical Methods in Efficiency Calibration and Uncertainty Estimation in Gamma Based Non-Destructive Assay - 12311

Mathematical methods are being increasingly employed in the efficiency calibration of gamma based systems for non-destructive assay (NDA) of radioactive waste and for the estimation of the Total Measurement Uncertainty (TMU). Recently, ASTM (American Society for Testing and Materials) released a standard guide for use of modeling passive gamma measurements. This is a testimony to the common use and increasing acceptance of mathematical techniques in the calibration and characterization of NDA systems. Mathematical methods offer flexibility and cost savings in terms of rapidly incorporating calibrations for multiple container types, geometries, and matrix types in a new waste assay system or a system that may already be operational. Mathematical methods are also useful in modeling heterogeneous matrices and non-uniform activity distributions. In compliance with good practice, if a computational method is used in waste assay (or in any other radiological application), it must be validated or benchmarked using representative measurements. In this paper, applications involving mathematical methods in gamma based NDA systems are discussed with several examples. The application examples are from NDA systems that were recently calibrated and performance tested. Measurement based verification results are presented. Mathematical methods play an important role in the efficiency calibration of gamma based NDA systems. This is especially true when the measurement program involves a wide variety of complex item geometries and matrix combinations for which the development of physical standards may be impractical. Mathematical methods offer a cost effective means to perform TMU campaigns. Good practice demands that all mathematical estimates be benchmarked and validated using representative sets of measurements. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

An automatic performance model-based scheduling tool for coupled climate system models

The prediction of the climate system is highly depended on the efficient integration of observations and simulations of the Earth. This is regarded as a canonical example of the cyber-physical system. The climate system model, the simulation engine in this cyber-physical system, is one of most challenging applications in scientific computing. It utilizes the multi-physics simulation that couples multiple components, conducts decadal to millennium simulations, and has long been an important application on supercomputers. However, current climate system models suffer from the inefficient task scheduling methods resulting in an intolerable simulation time. Take the Community Earth System Model (CESM), the most widely used climate system model, as an example, one major reason that CESM suffers from bad performances is the huge overhead to rationally distribute processes among the coupled heterogeneous components. According to the report of NCAR, every percent improvement in CESM performance frees up to the equivalent of $250,000 in computing resources in their scientific experiments. To address such challenge, our paper firstly constructs a lightweight and accurate performance model for effectively capturing and predicting the heterogeneous time-to-solution performance of end-to-end CESM components with a given simulation configuration. Then, based on the performance model, we further propose an efficient scheduling strategy based on rectangular packing method to determine the best process layout among different components, and the process numbers assigned to each component. Our evaluations show that we can achieve 58% average run time reductions on CESM comparing to the widely used sequential process layout for a scale of 144 to 480 cores on typical CPU clusters. And we can save 4 million CPU hours when we conduct one standard scientific experiment (a 2870-year simulation), which equals to save $40,089 with a charge of $0.01 per CPU hour. Meanwhile, 26% extra performance improvements could also be gained in our methods comparing to the heuristic branch and bound algorithm with the guidance of the known curve-fitting performance model.

58 GEOSCIENCES↗

Integrating Analytical Solutions and U-Net Model for Predicting Groundwater Contaminant Plumes in Pump-and-Treat Systems

Pump-and-treat (P&T) is a common technique for groundwater remediation involving the extraction and treatment of contaminated water above ground. Optimizing the design and operation of the P&T well network is essential for maximizing the system’s effectiveness and efficiency. However, this optimization often necessitates many model evaluations, leading to computationally demanding tasks. This study introduces a novel approach that integrates analytical solutions for groundwater dynamics with the U-Net (Ronneberger et al., 2015) deep learning framework to predict groundwater contaminant plume migration under dynamic pumping conditions. By incorporating the Thiem equation (Thiem, 1906) into the input preprocessing, the U-Net model transforms sparse well data into a continuous spatial field that captures the hydraulic impacts of pumping activities. This integration enables the model to leverage both deep learning capabilities and classical physics-based groundwater theories, enhancing prediction accuracy and computational efficiency. These advancements can facilitate rapid, large-scale evaluations of P&T optimization simulations, allowing for timely and effective decision-making in well placement and system management. We demonstrate the model's robust performance across both simplified transient 2D models and a more complex 3D heterogeneous site model at the 200 West P&T facility at the Hanford Site. The U-Net-based model offers substantial computational advantages, reducing simulation times significantly compared to full physics-based models and providing a powerful tool for rapid site evaluation and P&T system optimization, such as evaluating alternative P&T well network designs. Our findings highlight the potential of advanced machine learning models to significantly enhance the efficiency and sustainability of groundwater remediation efforts, offering a novel application of U-Net architecture in environmental science.

Pump-and-treat↗

Development of a change management system

The complexity and interdependence of software on a computer system can create a situation where a solution to one problem causes failures in dependent software. In the computer industry, software problems arise and are often solved with 'quick and dirty' solutions. But in implementing these solutions, documentation about the solution or user notification of changes is often overlooked, and new problems are frequently introduced because of insufficient review or testing. These problems increase when numerous heterogeneous systems are involved. Because of this situation, a change management system plays an integral part in the maintenance of any multisystem computing environment. At the NASA Ames Advanced Computational Facility (ACF), the Online Change Management System (OCMS) was designed and developed to manage the changes being applied to its multivendor computing environment. This paper documents the research, design, and modifications that went into the development of this change management system (CMS).

Parks, Cathy Bonifas↗

A Latency-Tolerant Partitioner for Distributed Computing on the Information Power Grid

NASA's Information Power Grid (IPG) is an infrastructure designed to harness the power of graphically distributed computers, databases, and human expertise, in order to solve large-scale realistic computational problems. This type of a meta-computing environment is necessary to present a unified virtual machine to application developers that hides the intricacies of a highly heterogeneous environment and yet maintains adequate security. In this paper, we present a novel partitioning scheme. called MinEX, that dynamically balances processor workloads while minimizing data movement and runtime communication, for applications that are executed in a parallel distributed fashion on the IPG. We also analyze the conditions that are required for the IPG to be an effective tool for such distributed computations. Our results show that MinEX is a viable load balancer provided the nodes of the IPG are connected by a high-speed asynchronous interconnection network.

Das, Sajal K.↗

Direct Simulations of Coupled Transport and Reaction on Nano-Scale X-Ray Computed Tomography Images of Platinum Group Metal-Free Catalyst Cathodes

The nano/micro-scale geometry of polymer electrolyte fuel cell (PEFC) catalyst layers critically affects cell performance. The small length scales and complex structure of these composite layers make it challenging to analyze cell performance and physics at the particle scale by experiment. We present a computational method to simulate transport and chemical reaction phenomena at the pore/particle-scale and apply it to a PEFC cathode with platinum group metal free (PGM-free) catalyst. Here, we numerically solve the governing equations for the physics with heterogeneous oxygen diffusion coefficient and proton conductivity evaluated using the actual electrode structure and ionomer distribution obtained using nano-scale resolution X-ray computed tomography (nano-CT). Using this approach, the oxygen concentration and electrolyte potential distributions imposed by the oxygen reduction reaction are solved and the impact of the catalyst layer structure on performance is evaluated.

36 MATERIALS SCIENCE↗

Computational optimization of electric fields for better catalysis design

Although the ubiquitous role that long-ranged electric fields play in catalysis has been recognized, it is seldom used as a primary design parameter in the discovery of new catalytic materials. Here in this paper, we illustrate how electric fields have been used to computationally optimize biocatalytic performance of a synthetic enzyme, and how they could be used as a unifying descriptor for catalytic design across a range of homogeneous and heterogeneous catalysts. Although focusing on electrostatic environmental effects may open new routes toward the rational optimization of efficient catalysts, much more predictive capacity is required of theoretical methods to have a transformative impact in their computational design — and thus experimental relevance — when using electric field alignments in the reactive centres of complex catalytic systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Green Rust Reduction of Chromium Part 2: Comparison of Heterogeneous and Homogeneous Chromate Reduction

White and green rusts are the active chemical reagents of buried scrap iron pollutant remediation. In this work, a comparison of the initial electron-transfer step for the reduction of CrO{sub 4}{sup -2} by Fe{sub (aq)}{sup 2+} and Fe(OH){sub 2}(s) is presented. Using hybrid density functional theory and Hartree-Fock cluster calculations for the aqueous reaction, the rate constant for the homogeneous reduction of chromium by ferrous iron was determined to be 5 x 10{sup -2} M{sup -1} s{sup -1} for the initial electron transfer. Using a combination of Hartree-Fock slab and cluster calculations for the heterogeneous reaction, the initial electron transfer for the heterogeneous reduction of chromium by ferrous iron was determined to be 1 x 10{sup 2} s{sup -1}. The difference in rates is driven by the respective free energies of reaction: 33.4 vs -653.2 kJ/mol. This computational result is apparently the opposite of what has been observed experimentally, but further analysis suggests that these results are fully convergent with experiment. The experimental heterogeneous rate is limited by surface passivation from slow intersheet electron transfer, while the aqueous reaction may be an autocatalytic heterogeneous reaction involving the iron oxyhydroxide product. As a result, it is possible to produce a clear model of the pollutant reduction reaction sequence for these two reactants.

36 MATERIALS SCIENCE↗

Widely tunable, heterogeneously integrated quantum-dot O-band lasers on silicon

Heterogeneously integrated lasers in the O-band are a key component in realizing low-power optical interconnects for data centers and high-performance computing. Quantum-dot-based materials have been particularly appealing for light generation due to their ultralow lasing thresholds, small linewidth enhancement factor, and low sensitivity to reflections. Here, we present widely tunable quantum-dot lasers heterogeneously integrated on silicon-on-insulator substrate. The tuning mechanism is based on Vernier dual-ring geometry, and a 47 nm tuning range with 52 dB side-mode suppression ratio is observed. These parameters show an increase to 52 nm and 58 dB, respectively, when an additional wavelength filter in the form of a Mach–Zehnder interferometer is added to the cavity. The Lorentzian linewidth of the lasers is measured as low as 5.3 kHz.

Malik, Aditya (ORCID:0000000334487577)↗

Effects of platinum stagnation surface on the lean extinction limits of premixed methane/air flames at moderate surface temperatures

A stagnation flow reactor was used to study the effects of platinum on the lean flammability limits of atmospheric pressure premixed methane/air flames at moderate stagnation surface temperatures. Experimental and computational methods were used to quantify the equivalence ratio at the lean extinction limit ({phi}{sub ext}) and the corresponding stagnation surface temperature (T{sub s}). A range of flow rates (57-90 cm/s) and corresponding strain rates were considered. The results indicate that the gas-phase methane/air flames are sufficiently strong relative to the heterogeneous chemistry for T{sub s} conditions less than 750 K that the platinum does not affect {phi}{sub ext}. The computational results are in good agreement with the experimentally observed trends and further indicate that higher reactant flow rates (>139 cm/s) and levels of dilution (>{proportional_to}10% N{sub 2}) are required to weaken the gas-phase flame sufficiently for surface reaction to play a positive role on extending the lean flammability limits. (author)

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Deformation mechanisms, defects, heat treatment, and thermal conductivity in large grain niobium

The physical and mechanical metallurgy underlying fabrication of large grain cavities for superconducting radio frequency accelerators is summarized, based on research of 1) grain orientations in ingots, 2) a metallurgical assessment of processing a large grain single cell cavity and a tube, 3) assessment of slip behavior of single crystal tensile samples extracted from a high purity ingot slice before and after annealing at 800 °C / 2 h, 4) development of crystal plasticity models based upon the single crystal experiments, and 5) assessment of how thermal conductivity is affected by strain, heat treatment, and exposure to hydrogen. Because of the large grains, the plastic anisotropy of deformation is exaggerated, and heterogeneous strains and localized defects are present to a much greater degree than expected in polycrystalline material, making it highly desirable to computationally anticipate potential forming problems before manufacturing cavities.

36 MATERIALS SCIENCE↗

Anomalous small-angle X-ray scattering of nanoporous two-phase atomistic models for amorphous silicon–germanium alloys

The present work deals with a detailed analysis of the anomalous small-angle X-ray scattering in amorphous silicon–germanium alloy using the simulation technique. We envisage the nanoporous two-phase alloy model consisting in a mixture of Ge-rich and Ge-poor domains and voids at the nanoscale. By substituting Ge atoms for Si atoms in nanoporous amorphous silicon network, compositionally heterogeneous alloys are generated with various composition-contrasts between the two phases. After relaxing the as-generated structure, we compute its radial distribution function, and then we deduce by the Fourier transform technique its anomalous X-ray scattering pattern. Using a smoothing procedure, the computed X-ray scattering patterns are corrected for the termination errors due to the finite size of the model, allowing so a rigorous quantitative analysis of the anomalous small-angle scattering. Our simulation shows that, as expected, the anomalous small-angle X-ray scattering technique is a tool of choice for characterizing compositional heterogeneities coexisting with structural inhomogeneities in an amorphous alloy. Furthermore, the sizes of the compositional nanoheterogeneities, as measured by anomalous small-angle X-ray scattering technique, are X-ray energy independent. A quantitative analysis of the separated reduced anomalous small-angle X-ray scattering, as defined in this work, provided a good estimate of their size.

36 MATERIALS SCIENCE↗

Mathematical and Computational Challenges in Population Biology and Ecosystems Science

Mathematical and computational approaches provide powerful tools in the study of problems in population biology and ecosystems science. The subject has a rich history intertwined with the development of statistics and dynamical systems theory, but recent analytical advances, coupled with the enhanced potential of high-speed computation, have opened up new vistas and presented new challenges. Key challenges involve ways to deal with the collective dynamics of heterogeneous ensembles of individuals, and to scale from small spatial regions to large ones. The central issues-understanding how detail at one scale makes its signature felt at other scales, and how to relate phenomena across scales-cut across scientific disciplines and go to the heart of algorithmic development of approaches to high-speed computation. Examples are given from ecology, genetics, epidemiology, and immunology.

Levin, Simon A.↗

A pseudo-spectral method for the simulation of poro-elastic seismic wave propagation in 2D polar coordinates using domain decomposition

We present a novel numerical approach for the comprehensive, flexible, and accurate simulation of poro-elastic wave propagation in 2D polar coordinates. An important application of this method and its extensions will be the modeling of complex seismic wave phenomena in fluid-filled boreholes, which represents a major, and as of yet largely unresolved, computational problem in exploration geophysics. In view of this, we consider a numerical mesh, which can be arbitrarily heterogeneous, consisting of two or more concentric rings representing the fluid in the center and the surrounding porous medium. The spatial discretization is based on a Chebyshev expansion in the radial direction and a Fourier expansion in the azimuthal direction and a Runge–Kutta integration scheme for the time evolution. A domain decomposition method is used to match the fluid–solid boundary conditions based on the method of characteristics. This multi-domain approach allows for significant reductions of the number of grid points in the azimuthal direction for the inner grid domain and thus for corresponding increases of the time step and enhancements of computational efficiency. The viability and accuracy of the proposed method has been rigorously tested and verified through comparisons with analytical solutions as well as with the results obtained with a corresponding, previously published, and independently benchmarked solution for 2D Cartesian coordinates. Finally, the proposed numerical solution also satisfies the reciprocity theorem, which indicates that the inherent singularity associated with the origin of the polar coordinate system is adequately handled.

97 MATHEMATICS AND COMPUTING↗

CryoDRGN-AI: neural ab initio reconstruction of challenging cryo-EM and cryo-ET datasets

Proteins and other biomolecules form dynamic macromolecular machines that are tightly orchestrated to move, bind, and perform chemistry. Cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET) can access the intrinsic heterogeneity of these complexes and are therefore key tools for understanding their function. However, 3D reconstruction of the collected imaging data presents a challenging computational problem, especially without any starting information, a setting termed ab initio reconstruction. Here, in this study, we introduce cryoDRGN-AI, a method leveraging an expressive neural representation and combining an exhaustive search strategy with gradient-based optimization to process challenging heterogeneous datasets. Using cryoDRGN-AI, we reveal new conformational states in large datasets, reconstruct previously unresolved motions from unfiltered datasets, and demonstrate ab initio reconstruction of biomolecular complexes from in situ data. With this expressive and scalable model for structure determination, we hope to unlock the full potential of cryo-EM and cryo-ET as a high-throughput tool for structural biology and discovery.

Levy, Axel [Stanford Univ., CA (United States); SL↗