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At least 433 records · Page 24

CoLoRe: fast cosmological realisations over large volumes with multiple tracers

We present CoLoRe, a public software package to efficiently generate synthetic realisations of multiple cosmological surveys.CoLoRe can simulate the growth of structure with different degrees of accuracy, with the current implementation supporting lognormal fields, first, and second order Lagrangian perturbation theory.CoLoRe simulates the density field on an all-sky light-cone up to a desired maximum redshift, and uses it to generate multiple 2D and 3D maps: galaxy positions and velocities, lensing (shear, magnification, convergence), integrated Sachs-Wolfe effect, line intensity mapping, and line of sight skewers for simulations of the Lyman-α forest. We test the accuracy of the simulated maps against analytical theoretical predictions, and showcase its performance with a multi-survey simulation including DESI galaxies and quasars, LSST galaxies and lensing, and SKA intensity mapping and radio galaxies. We expect CoLoRe to be particularly useful in studies aiming to characterise the impact of systematics in multi-experiment analyses, quantify the covariance between different datasets, and test cross-correlation pipelines for near-future surveys.

79 ASTRONOMY AND ASTROPHYSICS↗

AR reactor neutronics multi-code validation*

The affordable, robust, compact (ARC) reactor is a tokamak fusion reactor concept currently under development by Commonwealth Fusion Systems and Massachusetts Institute of Technology. There are three important neutronics considerations for the operation of the ARC reactor: (1) breeding of enough tritium in the blanket to sustain the D–T reaction in the plasma; (2) ensuring low fluence on the superconducting toroidal field coils; and (3) assessing neutron volumetric heating in structural components. Here, this work aims to perform a validation of the neutronics analysis approach by code-to-code comparison. State-of-the-art software stacks are employed for the neutronics analysis of the ARC reactor, and a computer-aided design (CAD) model is used directly for Monte Carlo (MC) neutron transport calculations. Three software stacks, Attila-MCNP, OpenMC-DAGMC, and Shift-DAGMC, are used to perform neutronic analyses of a 90° sector CAD model of the ARC reactor. In conclusion, results show that the flux tallies calculated by the three software stacks are very close. Also, the volumetric heating and tritium breeding values have less than 0.6% relative difference between codes.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Performance Testing and Assessment of Protection Scheme Using Real-Time Hardware-in-the-Loop and IEC 61850 Standard

The main challenge of the microgrid is to design a suitable protection scheme due to the complexity of the architecture of the microgrid. The importance of the proposed protection technique is threefold. First, it presents a co-simulation platform to integrate between a simulated model on power system computer aided design (PSCAD)/real time digital simulator computer aided design (RSCAD) software’s and physical devices schweitzer engineering laboratories (SEL) 421-7 relays to protect the microgrid that includes different resources connected based on inverter interface. Second, it presents a comprehensive hardware/software setup to test the protective relays in a closed loop system and shows how to configure the protective relay’s International Electrotechnical Commission 61850 communications. Third, IEEE 1588 standard is used to provide sub nanoseconds latency between the simulated model that emulated on real time digital simulator (RTDS) and the external devices. Also, the measurement signals are synchronized between RTDS and the external devices using giga-transceiver synchronization card (GTSYNC) interface card and SEL-2488 satellite-synchronized network clock. The results showed that the co-simulation infrastructure introduces a highly dependable design, analysis, and testing environment for cyber and physical data flow in the system. Besides that, the voltages at ac/dc sides and frequency at fault condition were maintained due to the energy storage device contributions at different modes of operation.

42 ENGINEERING↗

Effect of frequency and applied voltage of an atmospheric-pressure dielectric-barrier discharge on breakdown and hydroxyl-radical generation with a liquid electrode

This work examines the effect of the frequency and peak applied voltage on hydroxyl-radical generation in a dielectric-barrier plasma discharge between a metallic needle electrode and one electrode covered with dielectric. The authors examine a system that can expose up to 96 liquid samples in an automated fashion without human intervention beyond setting the initial software configuration. Then, hydroxylradical concentration, measured through coumarin fluorescence, was measured for 5 s plasma exposures generated under different highvoltage conditions with frequencies from 2 to 16 kHz and amplitudes from 4 to 9 kV. Their results show that an increase in frequency and/or applied voltage, within the range prescribed above and the limits of the high-voltage power supply, can yield up to a 150% increase in fluorescence with an equivalent hydroxyl-radical increase. Applications using typical previous methods, such as the Fenton Reaction, are limited in that they continuously generate hydroxyl radicals over millisecond and longer intervals. These results establish the electrical parameters that can now be applied to polymers, like proteins, which show three dimensional structures that are flexible and fluctuate on a microsecond and nanosecond time scale, with hydroxyl-radical generation on this time scale using this device. Additionally, plasma exposures may be optimized for a great variety of proteins, devices and techniques, where hydroxyl-radical generation is of utmost importance, reducing exposure time and potential subjection of samples to harmful side effects.

42 ENGINEERING↗

pnnl-predictive-phenomics/concerto

This software was developed to solve the problem of curating and validating individual metabolic models and combining them into different consortia.

Pino, James↗

Innovations in optimization and control of accelerators using methods of differential geometry and genetic algorithms (Final Report)

Online tuning of particle accelerators is necessary in order to achieve optimal machine performance. However, it is also a major challenge due to the large parameter space which must be searched and the fact that many of the desir- able objectives compete with one another, and so will not reach their optimal values simultaneously. In order to mitigate these issues, we have explored using dimension-reduction techniques to reduce the size of the parameter space which must be searched and multi-objective genetic algorithms to obtain the sets of tuning parameters which provide pareto-optimal values for the objectives. These methods have enabled us to obtain improved values of the vertical emittance at the Cornell Electron Storage Ring (CESR), and to do so with greater control of orbit errors. Algorithmic tuning is a multidisciplinary endeavour, requiring expertise in beam dynamics, diagnostics, control systems and computer science, and thus a key practical problem is to formulate a common language in which experts with different specialties can communicate. We developed a solution to this problem in the form of a generic accelerator software interface that allows for rapid prototyping of optimization and control algorithms. Our interface is built on the Experimental Physics and Industrial Control Systems (EPICS) and makes possible testing control code in simulation before deployment on real accelerators, as well as deployment of third-party optimization code.

43 PARTICLE ACCELERATORS↗

Creation of a Weather Drivers Test Suite for Inclusion in ASHRAE Standard 140

Weather conditions are an important boundary condition for building performance simulation (BPS) calculations. For existing test cases in ASHRAE Standard 140 "Method of Test for Evaluating Building Performance Simulation Software" (ANSI/ASHRAE 2020), it was assumed that the software being tested could adequately read and interpret the weather data in the provided standard weather files. As differences between the programs have been reduced and as more programs have shifted to sub-hourly time steps this assumption has become more stretched. To address these concerns a new test suite testing a program's ability to read and interpret the data from a standard weather file was developed. The purpose of the test suite is to test the use of the typical data used from standard weather files.

54 ENVIRONMENTAL SCIENCES↗

Scalability of high-performance PDE solvers

Performance tests and analyses are critical to effective high-performance computing software development and are central components in the design and implementation of computational algorithms for achieving faster simulations on existing and future computing architectures for large-scale application problems. In this article, we explore performance and space-time trade-offs for important compute-intensive kernels of large-scale numerical solvers for partial differential equations (PDEs) that govern a wide range of physical applications. We consider a sequence of PDE-motivated bake-off problems designed to establish best practices for efficient high-order simulations across a variety of codes and platforms. We measure peak performance (degrees of freedom per second) on a fixed number of nodes and identify effective code optimization strategies for each architecture. In addition to peak performance, we identify the minimum time to solution at 80% parallel efficiency. The performance analysis is based on spectral and p-type finite elements but is equally applicable to a broad spectrum of numerical PDE discretizations, including finite difference, finite volume, and h-type finite elements.

97 MATHEMATICS AND COMPUTING↗

Multiparametric optical label-free imaging to analyze plant cell wall assembly and metabolism. (Final Report)

Plant tissues are often considered not ideal for fluorescence imaging because of the pervasive intrinsic fluorescence of many plant metabolites and the intricate interactions with light of the many semi-crystalline polymers at the cell wall. Our project aims to take advantage of this observed shortcoming by developing a label-free, optical microscopy platform for characterizing multiple fingerprints of important cell wall components and stress-related, at subcellular scale resolution. The new imaging system can collect fingerprints from both emitted and scattered light that can inform on the chemical nature, subcellular distribution, anisotropy, and molecular environment of multiple cell wall components in intact plant tissues. We are combining these imaging capabilities with computational tools that enable correlated registration, integration, and analysis. This fully integrated, multiparametric optical system will be used to address biological problems connected to cell wall assembly in grasses. This includes a focus on developmental and environmental variation of cell wall impregnation with silica, lignin, suberin, and cutin in different tissues and cell types. Our research plan comprises three main goals: (1) To develop an accessible imaging platform and associated open-source software able to extract and integrate fingerprints from fluorescence-associated (multispectral emission, lifetime, and polarization), wide-field polarimetry, second harmonic generation (SHG), and stimulated Raman scattering signals (SRS); (2) To determine unique combination of fingerprints for various cell wall components and selected metabolites; (3) To analyze the process of cell wall silicification in grasses and determine how silicification affects cell wall properties and lignin, cutin, and suberin deposition in other cell types under differ stress conditions.

59 BASIC BIOLOGICAL SCIENCES↗

Reproducibility of protein x-ray diffuse scattering and potential utility for modeling atomic displacement parameters

Protein structure and dynamics can be probed using x-ray crystallography. Whereas the Bragg peaks are only sensitive to the average unit-cell electron density, the signal between the Bragg peaks—diffuse scattering—is sensitive to spatial correlations in electron-density variations. Although diffuse scattering contains valuable information about protein dynamics, the diffuse signal is more difficult to isolate from the background compared to the Bragg signal, and the reproducibility of diffuse signal is not yet well understood. We present a systematic study of the reproducibility of diffuse scattering from isocyanide hydratase in three different protein forms. Both replicate diffuse datasets and datasets obtained from different mutants were similar in pairwise comparisons (Pearson correlation coefficient ≥0.8). The data were processed in a manner inspired by previously published methods using custom software with modular design, enabling us to perform an analysis of various data processing choices to determine how to obtain the highest quality data as assessed using unbiased measures of symmetry and reproducibility. The diffuse data were then used to characterize atomic mobility using a liquid-like motions (LLM) model. This characterization was able to discriminate between distinct anisotropic atomic displacement parameter (ADP) models arising from different anisotropic scaling choices that agreed comparably with the Bragg data. Our results emphasize the importance of data reproducibility as a model-free measure of diffuse data quality, illustrate the ability of LLM analysis of diffuse scattering to select among alternative ADP models, and offer insights into the design of successful diffuse scattering experiments.

59 BASIC BIOLOGICAL SCIENCES↗

Calculating Ti-6Al-4V β Transus Through a Chemistry-Based Equation Derived from Combined Element Binary Phase Diagrams

A mathematical model was developed to correlate the relationship between titanium alloying elements (Al, O, N, C, V, and Fe) in Ti-6Al-4V, and the resulting beta transus temperature (β{sub t}). The model was produced by analyzing the slope of the lines separating the alpha + beta (α + β) and beta (β) phase fields on combined element binary phase diagrams generated through the Pandat modeling software. Experimental results showed a strong agreement between the baseline data, obtained through differential thermal analysis (DTA), and the calculated β{sub t}, determined by measuring the chemistry at a location adjacent to the DTA sample. The difference between the calculated β{sub t} and the baseline DTA data was approximately ± 10 °F (± 5.56 °C). The thermodynamically ideal β{sub t} temperature was additionally modeled for each set of chemistries through the Pandat software. These results were compared to the β{sub t} temperatures determined through the chemistry-based equation and DTA methods.

36 MATERIALS SCIENCE↗

PRIME: a real-time cyber-physical systems testbed: from wide-area monitoring, protection, and control prototyping to operator training and beyond

As the power grid continues to evolve with advanced wide-area monitoring, protection, and control (WAMPAC) algorithms, there is an increasing need for realistic testbed environments with industry-grade software and hardware-in-the-loop (HIL) to perform verification and validation studies. Such testbed environments serve as ideal platforms to perform WAMPAC prototyping, operator training, and also to study the impacts of different types of cyberattack scenarios on the operation of the grid. In this paper, we introduce PRIME (PNNL cybeR physIcal systeMs tEstbed): the testbed that integrates real-time transmission system simulator with commercial industry grade energy management system (EMS) software and remote hardware-in-the-loop (RHIL). PRIME is an end-to-end, modular testbed that allows high-fidelity RHIL experimentation of a power system. We present two detailed case studies (fault location and clearing in transmission system, and operator training) to showcase the capabilities of our PRIME testbed. Finally, we briefly discuss some of the potential limitations of our testbed in terms of scalability and flexibility to setup larger test systems and identify directions for future work to address those limitations.

42 ENGINEERING↗

A Numerical Tool for the Design of Enhanced Geothermal Reservoirs based on Modeling of Thermo-Hydro-Mechanical Processes and Explicit Representation of 3D Discrete Fracture Networks

This project has developed a coupled thermo-hydro-mechanical numerical modeling tool for prediction of energy production from Enhanced Geothermal Reservoirs (EGS). The tool is unique because it can explicitly represent thousands of pre-existing natural fractures. The capabilities developed in this project were built on the already existing expertise of Itasca arising from thirty years of research and development in discrete element modeling of fractured rocks. A thermal module suitable for analysis of different heat transfer mechanisms in fractured rocks percolated by fluids was developed and coupled with the already existing hydro-mechanical calculation in 3DEC, a commercial software for analysis of jointed rock based on the discrete element method (DEM). The heat transfer module simulates heat conduction, heat advection by moving fluid in rock fractures, and convective heat exchange at the fracture walls between the rock and the moving fluid. Techniques for spatial discretization of heat transfer in EGS-type problems were evaluated, and a boundary layer meshing approach was developed. Also, given the significant differences in time scale of physical processes involved, temporal integration schemes for coupled advection-diffusion processes and coupled thermal-hydro-mechanical processes were developed by taking advantage of both implicit and explicit time integration and also optimizing the coupling intervals. These improvements were necessary for modeling EGS reservoirs. Also, the DFN capacities in 3DEC were extended to include a larger number of fractures. Research was carried out on approaches to simplify the DFN so that the model can meet computational demands, while preserving thermo-hydro-mechanical characteristics of the DFN. The developed modules were coupled with the already existing capabilities of 3DEC. The results were presented as a submitted conference paper (Riahi et al., 2018a). A series of benchmark and test examples showed the developed capabilities. Finally, the developed tool was tested for a large-scale reservoir model for longer periods of injection and production. The thermal draw-down curves were generated and presented. The project successfully met all the milestones laid out in the proposal. Results demonstrated the feasibility of developing a fast and reliable software for the EGS community to use for assessment and prediction of reservoir performance. Some of its applications include assessment of stimulated volume and produced temperature and power. It can also be used for improved engineering, design and optimization of EGS reservoirs as well as other unconventional resources such as shale gas. Finally, the 3D analysis presented in this study showed that simulating EGS reservoirs with tens of thousands of fractures is feasible, and confirmed that the developed tool can serve toward meeting the goals and objectives of Geothermal Technologies Office in overcoming technical barriers associated with commercial EGS development.

15 GEOTHERMAL ENERGY↗

A Preprocessing Tool for Enhanced Ion Mobility–Mass Spectrometry-Based Omics Workflows

The ability to improve the data quality of ion mobility–mass spectrometry (IM-MS) measurements is of great importance for enabling modular and efficient computational workflows and gaining better qualitative and quantitative insights from complex biological and environmental samples. We developed the PNNL PreProcessor, a standalone and user-friendly software housing various algorithmic implementations to generate new MS-files with enhanced signal quality and in the same instrument format. Different experimental approaches are supported for IM-MS based on Drift-Tube (DT) and Structures for Lossless Ion Manipulations (SLIM), including liquid chromatography (LC) and infusion analyses. The algorithms extend the dynamic range of the detection system, while reducing file sizes for faster and memory-efficient downstream processing. Specifically, multidimensional smoothing improves peak shapes of poorly defined low-abundance signals, and saturation repair reconstructs the intensity profile of high-abundance peaks from various analyte types. Further, other functionalities are data compression and interpolation, IM demultiplexing, noise filtering by low intensity threshold and spike removal, and exporting of acquisition metadata. Several advantages of the tool are illustrated, including an increase of 19.4% in lipid annotations and a two-times faster processing of LC-DT IM-MS data-independent acquisition spectra from a complex lipid extract of a standard human plasma sample. The software is freely available at https://omics.pnl.gov/software/pnnl-preprocessor.

59 BASIC BIOLOGICAL SCIENCES↗

time-resolved spectroscopy fit (trspecfit) v0.01

Analyze 2D time- and energy-resolved data, such as from a pump-probe spectroscopy experiment. User can select and input different peak shapes/ functions and background types to first fit a ground state/ unperturbed spectrum. This would be similar to how standard spectroscopy data is fit. Subsequently, to describe the time domain, users can choose functions that describe the temporal dynamics of one or more spectral features, such as a peak amplitude, peak position, etc. These time dynamics functions can be added or convoluted (e.g. describing an instrument response function) with each other. Functionality to integrate implicit variables leading to distributions of certain parameters/ functions is in development. Alternatively, 2D data can be analyzed one time step at a time to get an idea of the time dynamics of the system before deploying the global 2D fit described above. Typically people write custom software for this purpose. During my PhD I've seen five internal LBL and external researchers write one-off code in different languages to analyze time- and energy-resolved spectra. While this was specifically was for a laser pump - X-ray probe spectroscopy experiment, I'm trying to write a general package for the time-resolved spectroscopy community.

Mahl, Johannes [Lawrence Berkeley National Laborat↗

Enforcing End-to-end I/O Policies for Scientific Workflows using Software-Defined Storage Resource Enclaves

Data-intensive knowledge discovery requires scientific applications to run concurrently with analytics and visualization codes executing in situ for timely output inspection and knowledge extraction. Consequently, I/O pipelines of scientific workflows can be long and complex because they comprise many stages of analytics across different layers of the I/O stack of high-performance computing systems. Performance limitations at any I/O layer or stage can cause an I/O bottleneck resulting in greater than expected end-to-end I/O latency. In this paper, we present the design and implementation of a novel data management infrastructure called Software-Defined Storage Resource Enclaves (SIREN) at system level to enforce end-to-end policies that dictate an I/O pipeline's performance. SIREN provides an I/O performance interface for users to specify the desired storage resources in the context of in-situ analytics. If suboptimal performance of analytics is caused by an I/O bottleneck when data are transferred between simulations and analytics, schedulers in different layers of the I/O stack automatically provide the guaranteed lower bounds on I/O throughput. Lastly, our experimental results demonstrate that SIREN provides performance isolation among scientific workflows sharing multiple storage servers across two I/O layers (burst buffer and parallel file systems) while maintaining high system scalability and resource utilization.

97 MATHEMATICS AND COMPUTING↗

Connected and Learning Based Optimal Freight Management for Efficiency

The management of the future heterogenous fleet is a complex decision-making problem. The heterogenous fleet is emerging as decarbonization technologies are deployed by fleets toward lowering the freight operation emissions in Medium and Heavy-duty vehicles. Traditionally, in fleets characterized by a homogeneous Diesel Internal Combustion Engine (ICE) powertrain, the process of fleet planning and operational optimization unfolds sequentially without the necessity to account for powertrain and vehicle-specific characteristics during dispatch decisions. Fleets with trucks less than 5 years old tend to maintain stable vehicle efficiency with minimal operational reliability risks for fleet managers. However, the landscape changes with the incorporation of emerging powertrain technologies, which lack extensive operational data and service experiences. This includes technologies like hybrid, Electric, Fuel Cell, or alternative fuel ICE. Operational decisions for fleets featuring heterogeneous powertrain technologies and facing limited access to alternative fueling and charging stations become intricate, requiring careful consideration and optimization at each dispatch. The difference in efficiency characteristics of emerging technologies, their range limitations, and the restricted availability of charging/alternative fueling infrastructure, coupled with sensitivity to driving conditions (e.g., EV range reduction in low temperatures) and their impact on component aging (such as batteries), become pivotal factors influencing the reliable and efficient freight transportation. To make the path toward low emission freight transportation efficient and reliable, an AI-assisted fleet management software is developed in this project to help fleet managers in optimizing both adoption of emerging powertrain decarbonization, connected and automated technologies and also operating the fleet after such technologies are deployed as schematically. Freight transportation requirements are different depending on the cargos to be shipped, customer requirements and regions of operations. This further highlights the need for software and digital solutions to tailor deployment and operation of emerging powertrain, connectivity, and automation technologies toward the specific fleet operation requirements. The fleet management optimizer was also integrated with a model of the fleet to simulate the operation of the fleet over 1 year of the baseline fleet operation (250,000+ shipments) indicating the significance of day-to-day variations on emissions and energy consumption of a freight transportation fleet. The results demonstrate ≥20% improvement in freight efficiency in terms of WTW CO2 per ton-mile of cargo shipments while all fleet operation constraints are enforced, and the cost (CapEx and OpEx) is minimized.

33 ADVANCED PROPULSION SYSTEMS↗

Stereo-DIC Challenge 1.0 – Rigid Body Motion of a Complex Shape

Background Stereo-DIC is a widely used optical measurement technique that provides a dense full-field 3D measurement of the shape, displacement, and strain of a solid sample. When compared with 2D-DIC, Stereo-DIC provides greater flexibility and expands its use beyond flat, planar specimens. Furthermore, the widespread availability of commercial systems has led to the adoption of the technique throughout industry, academia, and government research labs. Objective Even though some research has been done to understand the effects of different experimental and stereo-DIC parameters, no reference is available to benchmark and compare the performance of current stereo-DIC algorithms to each other. Methods This paper provides the description and analysis of a carefully controlled 3D experiment and associated images used to compare the results from five subset based DIC software packages. Both the images and analysis codes used in this paper to compare the results are described here and are available for download and use for continued research. Results We show that over a very large range of motion, the 3D errors are very small, less than 80μm over a travel of ±20 mm out-of-plane and ±20 mm in-plane. While all codes performed similarly, there are important differences noted in the paper. Conclusion The image sets and results comparison software are hosted by the International DIC Society (www.iDICs.org) and are freely available for download and analysis for comparison with results in this paper. Furthermore, it is hoped that this set of images can be used for future research in improving stereo-DIC by future authors.

Algorithms comparison↗