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DOE OSTI2015

The Sim-SEQ Project: Comparison of Selected Flow Models for the S-3 Site

Sim-SEQ is an international initiative on model comparison for geologic carbon sequestration, with an objective to understand and, if possible, quantify model uncertainties. Model comparison efforts in Sim-SEQ are at present focusing on one specific field test site, hereafter referred to as the Sim-SEQ Study site (or S-3 site). Within Sim-SEQ, different modeling teams are developing conceptual models of CO2 injection at the S-3 site. In this paper, we select five flow models of the S-3 site and provide a qualitative comparison of their attributes and predictions. These models are based on five different simulators or modeling approaches: TOUGH2/EOS7C, STOMP-CO2e, MoReS, TOUGH2-MP/ECO2N, and VESA. In addition to model-to-model comparison, we perform a limited model-to-data comparison, and illustrate how model choices impact model predictions. We conclude the paper by making recommendations for model refinement that are likely to result in less uncertainty in model predictions.

Carbon sequestration↗

DOE OSTI2014

In situ molecular imaging of hydrated biofilm in a microfluidic reactor by ToF-SIMS

The first results of using a novel single channel microfluidic reactor to enable Shewanella biofilm growth and in situ characterization using time-of-flight secondary ion mass spectrometry (ToF-SIMS) in the hydrated environment are presented. The new microfluidic interface allows direct probing of the liquid surface using ToF-SIMS, a vacuum surface technique. The detection window is an aperture of 2 m in diameter on a thin silicon nitride (SiN) membrane and it allows direct detection of the liquid surface. Surface tension of the liquid flowing inside the microchannel holds the liquid within the aperture. ToF-SIMS depth profiling was used to drill through the SiN membrane and the biofilm grown on the substrate. In situ 2D imaging of the biofilm in hydrated state was acquired, providing spatial distribution of the chemical compounds in the biofilm system. This data was compared with a medium filled microfluidic reactor devoid of biofilm and dried biofilm samples deposited on clean silicon wafers. Principle Component Analysis (PCA) was used to investigate these observations. Our results show that imaging biofilms in the hydrated environment using ToF-SIMS is possible using the unique microfluidic reactor. Moreover, characteristic biofilm fatty acids fragments were observed in the hydrated biofilm grown in the microfluidic channel, illustrating the advantage of imaging biofilm in its native environment.

Environmental Molecular Sciences Laboratory↗

DOE OSTI2014

Preliminary Verification and Validation of WEC-Sim, an Open-Source Wave Energy Converter Design Tool: Preprint

To promote and support the wave energy industry, a wave energy converter (WEC) design tool, WEC-Sim, is being developed by Sandia National Laboratories and the National Renewable Energy Laboratory. In this paper, the WEC-Sim code is used to model a point absorber WEC designed by the U.S. Department of Energy's reference model project. Preliminary verification was performed by comparing results of the WEC-Sim simulation through a code-to-code comparison, utilizing the commercial codes ANSYS-AQWA, WaveDyn, and OrcaFlex. A preliminary validation of the code was also performed by comparing WEC-Sim simulation results to experimental wave tank tests.

16 TIDAL AND WAVE POWER↗

DOE OSTI2020

Development and Validation of Passive Yaw in the Open-Source WEC-Sim Code

A passive yaw implementation is developed, validated, and explored for the WEC-Sim, an open-source wave energy converter modeling tool that works within MATLAB/Simulink. The Reference Model 5 (RM5) is selected for this investigation, and a WEC-Sim model of the device is modified to allow yaw motion. A boundary element method (BEM) code was used to calculate the excitation force coefficients for a range of wave headings. An algorithm was implemented in WEC-Sim to determine the equivalent wave heading from a body’s instantaneous yaw angle and interpolate the appropriate excitation coefficients to ensure the correct time-domain excitation force. This approach is able to determine excitation force for a body undergoing large yaw displacement. For the mathematically simple case of regular wave excitation, the dynamic equation was integrated numerically and found to closely approximate the results from this implementation in WEC-Sim. A case study is presented for the same device in irregular waves. In this case, computation time is increased by 32x when this interpolation is performed at every time step. To reduce this expense, a threshold yaw displacement can be set to reduce the number of interpolations performed. A threshold of 0.01° was found to increase computation time by only 22x without significantly affecting time domain results. Similar amplitude spectra for yaw force and displacements are observed for all threshold values less than 1°, for which computation time is only increased by 2.2x.

50 EE - Wind and Water Power Program - Water (EE-4↗

DOE OSTI2022

HERO WEC V1.0 - WEC-Sim Model

This zip file contains the files that are needed to simulate NREL's HERO WEC (hydraulic and electric reverse osmosis wave energy converter). This requires the user to have already installed WEC-Sim. In addition to the standard toolboxes that are required to run WEC-Sim the user will also need the Simscape Fluids and Simscape Driveline packages. In the zip file you will find the following: - HEROV1_HPTO.slx: Simulink-based WEC Sim model of the first gen (V1.0) Hydraulic PTO (power take-off) that was designed for the HERO WEC - wecSimInputFile.m: Input file needed to run the model - userDefinedFunctionsMCR.m: MCR (multi condition run) script that is needed if a use wants to simulate multiple wave conditions. - geometry (folder): Includes the geometry file that is needed for visualization - hydroData (folder): Includes the required WAMIT data to run WEC-Sim

16 TIDAL AND WAVE POWER↗

DOE OSTI2024

Laboratory Upgrade Point Absorber WEC-Sim Model with MoorDyn Moorings

This dataset includes a WEC-Sim and MoorDyn model of the Laboratory Upgrade Point Absorber (LUPA). LUPA is an open-source wave energy converter designed and tested by Oregon State University. The files provided here constitute a stable LUPA configuration with three mooring lines. This model is 1/20 scale, optimized for the O.H. Hinsdale Wave Lab at Oregon State University. This model of LUPA adds MoorDyn functionality for more accurate mooring predictions and uses a more stable, updated version of LUPA's current physical configuration. This model is for WEC-Sim Version 6.0. A recent update of WEC-Sim has changed some functionality of MoorDyn such that this model will not work with WEC-Sim Version 6.1.

16 TIDAL AND WAVE POWER↗

DOE OSTI2016

In Situ Characterization of Hydrated Proteins in Water by SALVI and ToF-SIMS

We demonstrate in situ chemical imaging of protein biomolecules in the aqueous solution using System for Analysis at the Liquid Vacuum Interface (SALVI) and time-of-flight secondary ion mass spectrometry (ToF-SIMS). The fibronectin protein film was immobilized on the silicon nitride (SiN) membrane forming the SALVI detection area. During ToF-SIMS analysis, three modes of analysis were conducted including high spatial resolution mass spectra, two-dimensional (2D) imaging, and depth profiling. Mass spectra were acquired in both positive and negative modes. Deionized water was also analyzed as a reference sample. Our results show that fibronectin film in water has more distinct and stronger water cluster peaks compared to water alone. Characteristic peaks of amino acid fragments are also observable in the hydrated protein ToF-SIMS spectra. These results illustrate that protein molecule adsorption on a surface can be studied dynamically using SALVI and ToF-SIMS in the liquid environment.

chemical imaging↗

DOE OSTI2020

Development and Validation of Passive Yaw in the Open-Source WEC-Sim Code: Preprint

A passive yaw implementation is developed, validated, and explored for the Wave Energy Converter Simulator (WEC-Sim), an open-source wave energy converter modeling tool that works within MATLAB/Simulink. The Reference Model 5 (RM5) is selected for this investigation, and a WEC-Sim model of the device is modified to allow yaw motion. A boundary element method (BEM) code was used to calculate the excitation force coefficients for a range of wave headings. An algorithm was implemented in WEC-Sim to determine the equivalent wave heading from a body’s instantaneous yaw angle and interpolate the appropriate excitation coefficients to ensure the correct time-domain excitation force. This approach is able to determine excitation force for a body undergoing large yaw displacement. For the mathematically simple case of regular wave excitation, the dynamic equation was integrated numerically and found to closely approximate the results from this implementation in WEC-Sim. A case study is presented for the same device in irregular waves. In this case, computation time is increased by 32x when this interpolation is performed at every time step. To reduce this expense, a threshold yaw displacement can be set to reduce the number of interpolations performed. A threshold of 0.01 was found to increase computation time by only 22x without significantly affecting time domain results. Similar amplitude spectra for yaw force and displacements are observed for all threshold values less than or equal to 1, for which computation time is only increased by 2.2x.

50 EE - Wind and Water Power Program - Water (EE-4↗

DOE OSTI2014

Tandem MS and C 60 SIMS for the identification and characterization of lipids

The tandem MS capability of a C 60 ‐Qstar hybrid instrument was utilized for the characterization of glycerophosphocholine (GPC) lipids in positive ion mode SIMS. In general, the tandem MS of lipids is facilitated by cationization or reaction with alkali metal salts. Thus, the lipids were treated with LiTFA salt (lithiation) prior to mass spectrometric analysis. As a result of the sample treatment, cationized lipid molecular ions with lithium adducts were formed and were revealed by mass shifts of 6 Da relative to unreacted species in the SIMS spectra. The lithiated molecular ions of GPCs were then subjected to collision‐induced dissociation (CID) in tandem MS mode. Upon CID, fragments specifying the fatty acid and head group composition of the GPC lipid were generated and could be used for its structural characterization and identification. In addition, a more significant observation was revealed in the time‐of‐flight‐SIMS spectral data of the lithiated GPC. Here, we found that fragmentation was enhanced, and fragment ions similar to those produced by CID were present in the SIMS spectra. The implications of these results are discussed. Copyright © 2014 John Wiley & Sons, Ltd.

Durairaj, Anita↗

DOE OSTI2015

Assessing the potential of ToF-SIMS as a complementary approach to investigate cement-based materials — Applications related to alkali–silica reaction

In this study, the potential of time-of-flight secondary ion mass spectrometry (ToF-SIMS) for the application in cement-based materials is assessed in combination and comparison with scanning electron microscopy (SEM) and energy dispersive X-ray (EDX). Mortar, concrete and samples from model systems providing products formed by the alkali–silica reaction (ASR) were studied. ToF-SIMS provides qualitative data on alkalis in cases where EDX reaches its limits in regard to detectable concentration, lateral resolution and atomic number of the elements. Due to its high in-depth resolution of a few atomic monolayers, thin layers of reaction products can be detected on the surfaces and chemically analyzed with ToF-SIMS. Additionally, it delivers information on the molecular conformation within the ASR product, its hydrogen content and its isotope ratios, information not provided by EDX. Provided the samples are carefully prepared, ToF-SIMS opens up new possibilities in the analysis of cement-based materials.

36 MATERIALS SCIENCE↗

DOE OSTI2025

ToF-SIMS spectral analysis of pristine and neutron irradiated single crystal tungsten

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) has many promising features in studying materials including high spatial resolution and high mass accuracy of elements, molecules, and isotopes. Its ability to resolve isotopes is especially attractive in studying transmutation products of single crystal tungsten (SCW) post neutron irradiation. Tungsten (W) is a contender of plasma facing materials (PFMs) due to its high thermal and radiological stability. PFMs to be used in the construction of fusion vessels are subject to high temperature and neutron irradiation, resulting in changes to materials including transmutation, which ultimately impact material mechanical and thermal properties. We used IONTOF TOF.SIMS V instrument equipped with a 30 keV Bi 3 + primary ion beam to study pristine SCW and irradiated SCW speciemens. Scanning electron microscope coupled with focused ion beam (SEM-FIB) was used to reduce the dosage of neutron irradiated tungsten and prepare for specimens for SIMS analysis. Static ToF-SIMS spectra were obtained, and transmutation product peak identification was presented in this work. Identified molecules and molecular fragments were compared against isotope theoretical mass to charge ratios of tungsten, rhenium, osmium, and other relevant products. Our results show that ToF-SIMS provides a viable means to study transmutation products of W post neutron irradiation. Such applications are suitable to investigate transmutation effects on materials that are being considered and developed for fusion pilot plants.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Molecular Examination of Ion-Pair Competition in Alkaline Aluminate Solutions Using In Situ Liquid SIMS

Understanding the structure and composition of aluminate complexes in extremely alkaline systems such as Bayer liquors has received enormous attentions due to its fundamental and industrial importance. However, obtaining direct molecular information of the underlying ion-ion interactions using traditional approaches such as NMR or Raman spectroscopy is challenging due to the weakness of these interactions and/or their complex overlapping spectral signatures. Here, we exploit in situ liquid secondary ion mass spectrometry (SIMS) as a new approach and show how it enables new insights. In contrast with traditional techniques, using SIMS we succeeded in acquiring information on dominant ion clusters in these alkaline systems. In Na + /K + mixed alkaline aluminate solutions we clearly observe preferential formation of Na + -anion clusters over K + -anion clusters. Further, evaluation of these clusters by density functional theory (DFT) calculations shows that these structures are stable and that their relative bond energies are consistent with their observed SIMS signal intensity differences. This demonstrates a key advantage of in situ liquid SIMS for overcoming ambiguities obscuring important information in these systems on constituent molecular clusters defined by relatively weak ion pair competition and ion-solvent interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2018

Quantitative SIMS Imaging of Agar-Based Microbial Communities

After several decades of widespread use for mapping elemental ions and small molecular fragments in surface science, secondary ion mass spectrometry (SIMS) has emerged as a powerful analytical tool for molecular imaging in biology. Biomolecular SIMS imaging has primarily been used as a qualitative technique; although the distribution of a single analyte can be accurately determined, it is difficult to map the absolute quantity of a compound or even to compare the relative abundance of one molecular species to that of another. We describe a method for quantitative SIMS imaging of small molecules in agar-based microbial communities. The microbes are cultivated on a thin film of agar, dried under nitrogen, and imaged directly with SIMS. By use of optical microscopy, we show that the area of the agar is reduced by 26 ± 2% (standard deviation) during dehydration, but the overall biofilm morphology and analyte distribution are largely retained. We detail a quantitative imaging methodology, in which the ion intensity of each analyte is (1) normalized to an external quadratic regression curve, (2) corrected for isomeric interference, and (3) filtered for sample-specific noise and lower and upper limits of quantitation. The end result is a two-dimensional surface density image for each analyte. The sample preparation and quantitation methods are validated by quantitatively imaging four alkyl-quinolone and alkyl-quinoline N-oxide signaling molecules (including Pseudomonas quinolone signal) in Pseudomonas aeruginosa colony biofilms. Here, we show that the relative surface densities of the target biomolecules are substantially different from values inferred through direct intensity comparison and that the developed methodologies can be used to quantitatively compare as many ions as there are available standards.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2017

SIMS analyses of the oldest known assemblage of microfossils document their taxon-correlated carbon isotope compositions

Analyses by secondary ion mass spectroscopy (SIMS) of 11 specimens of five taxa of prokaryotic filamentous kerogenous cellular microfossils permineralized in a petrographic thin section of the ~3,465 Ma Apex chert of northwestern Western Australia, prepared from the same rock sample from which this earliest known assemblage of cellular fossils was described more than two decades ago, show their δ 13 C compositions to vary systematically taxon to taxon from -31‰ to -39‰. These morphospecies-correlated carbon isotope compositions confirm the biogenicity of the Apex fossils and validate their morphology-based taxonomic assignments. Perhaps most significantly, the δ 13 C values of each of the five taxa are lower than those of bulk samples of Apex kerogen (-27‰), those of SIMS-measured fossil-associated dispersed particulate kerogen (-27.6‰), and those typical of modern prokaryotic phototrophs (-25 ± 10‰). The SIMS data for the two highest δ 13 C Apex taxa are consistent with those of extant phototrophic bacteria; those for a somewhat lower δ 13 C taxon, with nonbacterial methane-producing Archaea; and those for the two lowest δ 13 C taxa, with methane-metabolizing γ-proteobacteria. Although the existence of both methanogens and methanotrophs has been inferred from bulk analyses of the carbon isotopic compositions of pre-2,500 Ma kerogens, these in situ SIMS analyses of individual microfossils present data interpretable as evidencing the cellular preservation of such microorganisms and are consistent with the near-basal position of the Archaea in rRNA phylogenies.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

SV-Sim: Scalable PGAS-based State Vector Simulation of Quantum Circuits

High-performance quantum circuit simulation in a classic HPC is still imperative in the NISQ era. Observing that the major obstacle of scalable state-vector quantum simulation arises from the massively fine-grained irregular data-exchange with remote nodes, in this paper we present SV-Sim to apply the emerging PGAS-based communication models (i.e., direct peer access for intra-node CPUs/GPUs and SHMEM for inter-node CPU/GPU clusters) for efficient scalable quantum circuit simulation. Through an orchestrated device functional pointer design, SV-Sim is able to abstract the quantum gate sets across various heterogeneous backends, including IBM/Intel/AMD CPUs, NVIDIA /AMD GPUs, and Intel MIC, in a unified framework, but still asserting outstanding performance and tractable interface to higher-level quantum programming environments, such as IBM Qiskit, Microsoft Q\# and Google Cirq. Circumventing the disability of polymorphism in GPUs and leveraging the device-initiated one-sided communication, SV-Sim can process dynamically synthesized quantum circuit in a single GPU/CPU kernel without the need of expensive JIT or runtime branching, significantly improving the performance and simplifying the programming complexity for the emerging variational quantum algorithms. Evaluations on NVIDIA A100-DGX-1, V100-DGX-2, AMD MI100, ALCF Theta, and OLCF Summit HPCs show that SV-Sim can delivery scalable performance on various state-of-the-art HPC platforms, offering a useful tool for quantum algorithm validation and verification.

Li, Ang↗

DOE OSTI2014

WEC-Sim (Wave Energy Converter - SIMulator)

WEC-Sim (Wave Energy Converter SIMulator) is a code developed by Sandia National Laboratories and the National Renewable Energy Laboratory to model wave energy converters (WECs) when they are subject to operational waves. The code is a time-domain modeling tool developed in MATLAB/Simulink using the multi-body dynamics solver SimMechanics. In WEC-Sim, WECs are modeled by connecting rigid bodies to one another with joint or constraint blocks from the WEC-Sim library. WEC-Sim is a publicly available, open-source code to model WECs.

Source record↗

DOE OSTI2024

MLEC-Sim: A Simulator for Evaluating Multi-Level Erasure Coding

We present MLEC-Sim, a sophisticated simulator for Multi-Level Erasure Coding (MLEC), developed in approximately 13 KLOC. The simulator is engineered to analyze the impact of various system configurations and erasure coding policies on system durability and network overhead. It supports a comprehensive range of parameters including disk capacity, disk I/O bandwidth, failure rates, network bandwidth, and system scale, accommodating various erasure coding approaches such as Single-Level Erasure Coding (SLEC), Multi-Level Erasure Coding (MLEC), and Local Reconstruction Codes (LRC). MLEC-Sim provides support for multiple chunk placement policies, including clustered parity and declustered parity, and encompasses a variety of repair methods like Repair-ALL, Repair-FCO, Repair-HYB, and Repair-MIN. It is capable of simulating disk failures through a variety of means, including distribution-based or trace-based mechanisms, and can handle complex multi-level (de)clustered placements and repair processes. A key feature of MLEC-Sim is its adoption of the splitting simulation method for evaluating system durabilities at extremely high levels, which are challenging to assess with traditional simulation approaches. This feature allows for a detailed evaluation of system resilience under a range of conditions, aiding in the selection of appropriate erasure coding solutions for enhancing system durability. MLEC-Sim contributes to the field of data storage and reliability by providing a tool for the detailed evaluation of the durability and efficiency of erasure coding configurations, intended for use by researchers and practitioners in the design and optimization of storage systems.

Wang, Meng↗

DOE OSTI2021

TEAMER - AquaHarmonics High Fidelity WEC Sim PTO and Control Model Validation, Test Logs and Results

Collaborative effort between AquaHarmonics, Sandia National Laboratories (SNL), and the National Renewable Energy Laboratory (NREL) to revise and validate Aquaharmonics' full wave to wire model, allowing for reduced uncertainty and increased understanding of design requirements of a utility scale wave energy converter (WEC). SNL and NREL in collaboration with AquaHarmonics, will set up and run WEC Simulator (WEC-Sim) models of the AquaHarmonics WEC, building off past model developments for inclusion of custom PTO (power take-off) dynamics. The intent is to review, update, and verify or validate a new WEC-Sim model against wave tank experimental data. Furthermore, the WEC-Sim model will be coupled to an energy storage system model to better understand the wave-to-wire functionality. This data set is described in the "Test Log" excel file. Please refer to that document for details on each specific test date/time, constraint parameters and model hardware setup details. Sim model can be found in the associated MHKDR link below.

16 TIDAL AND WAVE POWER↗