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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Studying microbially induced corrosion on glass using ToF-SIMS

Microbially induced corrosion (MIC) is an emerging topic that has huge environmental impacts, such as long-term evaluation of microbial interactions with radioactive waste glass, environmental cleanup and disposal of radioactive material, and weathering effects of microbes. Time-of-flight secondary ion mass spectrometry (ToF-SIMS), a powerful mass spectral imaging technique with high surface sensitivity, mass resolution, and mass accuracy, can be used to study biofilm effects on different substrates. Understanding how to prepare biofilms on MIC susceptible substrates is critical for proper analysis via ToF-SIMS. We present here a step-by-step protocol for preparing bacterial biofilms for ToF-SIMS analysis, comparing three biofilm preparation techniques: no desalination, centrifugal spinning (CS), and water submersion (WS). Comparisons of two desalinating methods, CS and WS, show a decrease in the media peaks up to 99% using CS and 55% using WS, respectively. Proper desalination methods also can increase biological signals by over four times for fatty acids using WS, for example. ToF-SIMS spectral results show chemical compositional changes of the glass exposed in a Paenibacillus polymyxa SCE2 biofilm, indicating its capability to probe microbiologically induced corrosion of solid surfaces. This represents the proper desalination technique to use without significantly altering biofilm structure and substrate for ToF-SIMS analysis. ToF-SIMS spectral results showed chemical compositional changes of the glass exposed by a Paenibacillus bacterial biofilm over 3-month inoculation. Finally, possible MIC products include various phosphate phase molecules not observed in any control samples with the highest percent increases when experimental samples were compared with biofilm control samples.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Review of recent WEC-Sim (v6.1) advanced features

WEC-Sim (Wave Energy Converter SIMulator) is an opensource software for modeling the motions, loads and power generation of wave energy converters. WEC-Sim performs simulations in the time domain using hydrodynamic coefficients calculated by boundary element method (BEM) frequency-domain potential flow solvers such as WAMIT, NEMOH, Capytaine, or Ansys AQWA. WEC-Sim development is ongoing, including various features, applications, and example cases used to demonstrate potential use-cases to meet the needs of the growing marine energy industry. Through input from a broad user base and an extensive team of developers and collaborators, new features of WEC-Sim are developed to expand the software’s use cases and improve overall functionality. Three new WEC-Sim features highlighted in this paper include updating WEC-Sim to be compatible with MoorDyn Version 2, incorporation of second order excitation loads (quadratic transfer functions) and allowing for dynamically changing hydrodynamics.

13 HYDRO ENERGY↗
DOE OSTI2020

The Cloud-resolving model Radar SIMulator (CR-SIM) Version 3.3: description and applications of a virtual observatory

Ground-based observatories use multi-sensor observations to characterize cloud and precipitation properties. One of the challenges is how to design strategies to best use these observations to understand these properties and evaluate weather and climate models. This paper introduces the Cloud resolving model Radar SIMulator (CR-SIM), which uses output from high-resolution cloud resolving models (CRMs) to emulate multi-wavelength, zenith-pointing, and scanning radar observables and multi-sensor (radar and lidar) products. CR-SIM allows direct comparison between an atmospheric model simulation and remote-sensing products using a forward-modeling framework consistent with the microphysical assumptions used in the atmospheric model. CR-SIM has the flexibility to easily incorporate additional microphysical modules, such as microphysical schemes and scattering calculations, and expand the applications to simulate multi-sensor retrieval products. In this paper, we present several applications of CR-SIM for evaluating the representativeness of cloud microphysics and dynamics in a CRM, quantifying uncertainties in radar-lidar integrated cloud products and multi-Doppler wind retrievals, and optimizing radar sampling strategy using observing system simulation experiments. These applications demonstrate the application of CR-SIM as a virtual observatory operator on high-resolution model output for a consistent comparison between model results and observations to aid interpretation of the differences and improve understanding of the representativeness errors due to the sampling limitations of the ground-based measurements. CR-SIM is licensed under the GNU GPL package and both the software and the user guide are publicly available to the scientific community.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2000

SIM Configuration Evolution

The Space Interferometry Mission (SIM) is a space-based 10 m baseline Michelson interferometer. Planned for launch in 2005 aboard a Delta III launch vehicle, or equivalent, its primary objective is to measure the positions of stars and other celestial objects with an unprecedented accuracy of 4 micro arc seconds. With such an instrument, tremendous advancement can be expected in our understanding of stellar and galactic dynamics. Using triangulation from opposite sides of the orbit around the sun (i.e. by using parallax) one can measure the distance to any observable object in our galaxy. By directly measuring the orbital wobble of nearby stars, the mass and orbit of planets can be determined over a wide range of parameters. The distribution of velocity within nearby galaxies will be measurable. Observations of these and other objects will improve the calibration of distance estimators by more than an order of magnitude. This will permit a much better determination of the Hubble Constant as well as improving our overall understanding of the evolution of the universe. SIM has undergone several transformations, especially over the past year and a half since the start of Phase A. During this phase of a project, it is desirable to perform system-level trade studies, so the substantial evolution of the design that has occurred is quite appropriate. Part of the trade-off process has addressed two major underlying architectures: SIM Classic; and Son of SIM. The difference between these two architectures is related to the overall arrangement of the optical elements and the associated metrology system. Several different configurations have been developed for each architecture. Each configuration is the result of design choices that are influenced by many competing considerations. Some of the more important aspects will be discussed. The Space Interferometry Mission has some extremely challenging goals: millikelvin thermal stability, nanometer stabilization of optics, picometer measurement of wavefront, and others. In order to meet these goals, a significant amount of technological development is required. Although there has been a program operating for about a decade developing technologies specifically to address the challenges of space-based interferometry, there still remains a tremendous effort to achieve the incredible accuracy required of SIM. The projected viability of some of these areas has influenced design choices during the evolution of the many configurations that have been developed. For instance, the perceived complexity of the IR laser metrology system used to measure and control the positions of key optical elements was the strongest discriminator between the two architectures, and led to a decision to select SOS rather than Classic in early 1998. More recently, an appreciation of the sensitivity to beam-walk within the SOS architecture is forcing a reconsideration of that decision. At the time of submission of this abstract, there is some hope that a full-aperture metrology system may alleviate this issue. In addition to describing the current configuration of SIM, the influence of a few selected areas on the evolution of the configuration will be discussed.

Aaron, Kim M.↗
NASA NTRS2004

SIM spectral characteristics and accuracy analysis

The Space Interferometry Mission (SIM) will perform global astrometry (full sky), local wide-angle (15 degree) and narrow-angle (1 degree) observations to search extra-solar planets, and can calibrate stellar and galactic evolution theories. The astrometric accuracy of the SIM mission depends on spectral characteristics of the optics, detectors and targets. This paper will discuss the photometric throughput of the SIM instrument, and analyze effects of wavefront errors, optical mismatches and control biases as a function of wavelength. The color dependence models of the instrument optics including mirrors, lenses, field-stop and beam-splitter are presented. The performances of different detectors with a variety of coatings are compared. A model of the SIM fringe spectrometer is created. For early and late types of stars, brightness dependency errors are analyzed for different combinations of optics and detectors. Visibility loss due to imperfect optics is investigated in detail. Based on the models of instrument and estimated visibilities, the astrometric accuracies for various kinds of stars are evaluated. It is important to emphasize that not only light sources, mirrors, lenses, field stop and detectors are all wavelength dependent, but also fringe visibility loss, wavefront error, optics control error, etc. are all a function of wavelengths. For the first time the estimate of SIM performance is based on spectral analysis of all factors above, rather than monochromatic approximations of detected fringes, or simply adopted constants. This paper summarizes the astrometric accuracies for a wide range of stars and various combinations of optical design and detector configurations. It has been verified that SIM has astrometric accuracy of about 4 μas for targets with different spectra.

Shao, Michael↗
NASA NTRS2006

The SIM PlanetQuest science program

SIM PlanetQuest (hereafter, just SIM) is a NASA mission to measure the angular positions of stars with unprecedented accuracy. We outline the main astrophysical science programs planned for SIM, and related opportunities for community participation. We focus especially on SIM’s ability to detect exoplanets as small as the Earth around nearby stars. The planned synergy between SIM and other planet-finding missions including Kepler and GAIA, and planetcharacterizing missions including the James Webb Space Telescope (JWST), Terrestrial Planet Finder – Coronagraph (TPF-C), and Terrestrial Planet Finder – Interferometer (TPF-I), is a key element in NASA’s Navigator Program to find Earth-like planets, determine their habitability, and search for signs of life in the universe. SIM's technology development is now complete and the project is proceeding towards a launch early next decade.

Marr, James C. IV↗
NASA NTRSDate not supplied

Comparing Analysis of Hydrogen Concentration in Astromaterials Nominally Anhydrous Minerals by Multiple SIMS

Secondary Ion Mass Spectrometry (SIMS) is utilized to determine hydrogen (H) concentration in astromaterials nominally anhydrous minerals (NAMs) and their inclusions [e.g., 1]. This data is interpreted to refine the volatile history of planetary bodies. Four instruments are being used to compare H concentration analysis: a large geometry SIMS (The University of Hawaiʻi Cameca IMS 1280), a compact SIMS (Arizona State University (ASU) Cameca IMS 6f), and two Cameca NanoSIMS 50L at ASU and NASA-Johnson Space Center (JSC). Results on the first three instruments are available. Although fundamentally similar, SIMS instruments and their modifications [2] may produce different values or pose advantages for H analysis, especially for shocked samples that are susceptible to contamination filling their fractures. New data from the IMS 1280 is reported, using its microchannel plate (MCP) to image high H signals in grain fractures during pre-sputtering to avoid them as much as possible. Between fractures, 16 OH/ 30 Si was measured with a Cs + 4 nA primary beam, 30 micron spot size, and central ~5x5 micron collection area. First order comparison of H concentration (reported in ppm H 2 O) is achieved on a terrestrial gem quality clinopyroxene (SLP114, 162±12 ppm H 2 O [3]), with 157±7 and 215±40 ppm H 2 O by the IMS 1280 and 6f respectively. SIMS comparison is then extended to analysis of two Martian shergottites: RBT 04262 and NWA 5789. Due to a dense fracture network (< 20 micron) in RBT 04262, only one clinopyroxene hosted glassy inclusion was analyzed (n=6, ≤1 ppm H 2 O), while six olivine grains in NWA 5789 (n=12, ≤ 2 ppm H 2 O) (1s ±0.21) were analyzed. Higher concentrations were obtained for RBT 04262 olivine by the ASU NanoSIMS 50L (up to 350 ppm H 2 O [4]), and IMS 6f (300+ ppm H 2 O, [5]), for which contamination in fractures could not be avoided. Work on the JSC NanoSIMS 50L will further develop the SIMS comparison.

J.-M. Dudley↗
DOE OSTI2023

Simulating Quantum Systems with NWQ-Sim on HPC

NWQ-Sim is a cutting-edge quantum system simulation environment designed to run on classical multi-node, multi-CPU/GPU heterogeneous HPC systems. In this work, we provide a brief overview of NWQ-Sim and its implementation in simulating quantum circuit applications, such as the transverse field Ising model. We also demonstrate how NWQ-Sim can be used to examine the effects of errors that occur on real quantum devices, using a combined device noise model. Moreover, NWQ-Sim is particularly well-suited for implementing variational quantum algorithms where circuits are dynamically generated. Therefore, we also illustrate this with the variational quantum eigensolver (VQE) for the Ising model. In both cases, NWQ-Sim's performance is comparable to or better than alternative simulators. We conclude that NWQ-Sim is a useful and flexible tool for simulating quantum circuits and algorithms, with performance advantages and noise-aware simulation capabilities.

Suh, In-Saeng↗
DOE OSTI2017

SIMS microanalysis of the Strelley Pool Formation cherts and the implications for the secular-temporal oxygen-isotope trend of cherts

The significance of oxygen isotope ratios in Archean chert has long been debated. Cherts from the c. 3.4 Ga Strelley Pool Formation (SPF) (Pilbara Craton, Western Australia) host some of the oldest stromatolite and microfossil evidence for life, but the genesis and timing of silica cements has been unclear. Field relations, petrography and a combination of laser fluorination and in-situ SIMS measurements of δ 18 O in quartz show that bedded cherts of the SPF were originally precipitated as carbonates and were later widely replaced by quartz. Three localities were studied and analyzed for δ 18 O(Qz) in chert: 1) Camel Creek: foliated, metamorphosed, bedded cherts and meter-scale black chert veins; 2) Unconformity Ridge and ABDP8 drill core: stromatolitic and bedded chert overlying basal detrital quartz sandstone; and 3) the Trendall locality: “bedded” stromatolitic chert replacing original dolomite, low temperature hydrothermal quartz, and mm- to decimeter-scale chert-quartz veins. Laser fluorination (mm-scale) values of δ18O(Qz) range from: 14.2 to 18.2‰ VSMOW at Camel Creek; 9.3 to 18.9‰ at Unconformity Ridge; and 13.7 to 25.7‰ at Trendall. Values of δ 18 O(Qz) in cm to decimeter-scale hydrothermal chert veins cutting bedded carbonates at Trendall range from ca. 15 to 16‰, whereas “bedded cherts” are 17 to 26‰. These laser data include the highest δ 18 O values reported for cherts in Paleoarchean sediments and are up to 4‰ higher than the upper limit of ~22‰ reported in other studies, in apparent contrast to the long-standing secular-temporal trend which shows such high δ 18 O only in younger chert. However, analysis by laser fluorination at the 1-mm scale cannot resolve microtextures seen petrographically. In contrast, in-situ SIMS analyses can resolve petrographic microtextures and show δ 18 O(Qz) at 10-μm scale have an even greater range of 7–31‰ in “bedded” cherts at the Trendall locality, up to 9‰ above the secular-temporal trend. Textures observed optically at the Trendall locality were classified as: microquartz, mesoquartz, chalcedony, megaquartz veins, and cavity megaquartz. SEM-CL imaging shows two generations of meso- and megaquartz; bright CL with well-developed growth zoning, and dark CL with massive or mottled texture. Microquartz is the earliest textural generation of quartz and has a maximum δ 18 O(Qz) of ~22‰ by SIMS. Dark-CL mesoquartz has similar δ 18 O to microquartz and is interpreted to also be early. Bright-zoned-CL mesoquartz, which formed post-Archean, has even higher δ 18 O, up to 29‰. Vein megaquartz crosscuts most quartz generations and has a restricted range of δ 18 O, mostly from 16 to 19‰. Chalcedony pseudomorphs rhombic cavities and fractures, lines the edges of veins, and has similar δ 18 O to veins (16–19‰). Late cavity megaquartz is bright and zoned by CL, grows into late open cavities, and has the highest δ 18 O(Qz) values reported from the Pilbara, up to 31.3‰. Thus, the highest-δ 18 O quartz cements at the Trendall locality are the youngest and may be related to weathering. Early silicification and the formation of microquartz, chalcedony and low δ 18 O mesoquartz occurred during low temperature hydrothermal activity in the Archean. None of the SPF quartz examined is interpreted to have formed as a direct precipitate from Paleoarchean seawater. Thus, values of δ 18 O(Qz) do not record either water chemistry or temperature of Archean oceans. In-situ SIMS analysis shows that high-δ 18 O(Qz) values above 22‰ are only found in late-forming cavity megaquartz and bright-zoned-CL mesoquartz at the Trendall locality. The SPF results from our sample suite demonstrate the ability to resolve complex history using detailed petrography and SIMS analysis. Similar studies may show equal complexity of δ 18 O(Qz) data for other localities that are interpreted to show secular-temporal trends for chert. The apparent increase of δ 18 O(Qz) through time may reflect differences in diagenesis, and/or an inherent and previously unrecognized sampling bias that compares fundamentally different populations of quartz, such as Archean hydrothermal chert from volcanic greenstone belts, with unrelated Phanerozoic biogenic quartz.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Molecular identification of wines using in situ liquid SIMS and PCA analysis

Composition analysis in wine is gaining increasing attention because it can provide information about the wine quality, source, and nutrition. In this work, in situ liquid secondary ion mass spectrometry (SIMS) was applied to 14 representative wines, including six wines manufactured by a manufacturer in Washington State, United States, four Cabernet Sauvignon wines, and four Chardonnay wines from other different manufacturers and locations. In situ liquid SIMS has the unique advantage of simultaneously examining both organic and inorganic compositions from liquid samples. Principal component analysis (PCA) of SIMS spectra showed that red and white wines can be clearly differentiated according to their aromatic and oxygen-contained organic species. Furthermore, the identities of different wines, especially the same variety of wines, can be enforced with a combination of both organic and inorganic species. Meanwhile, in situ liquid SIMS is sample-friendly, so liquid samples can be directly analyzed without any prior sample dilution or separation. Taken together, we demonstrate the great potential of in situ liquid SIMS in applications related to the molecular investigation of various liquid samples in food science.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2006

Results from SIM's Thermo-Opto-Mechanical (TOM3) Testbed

Future space-based optical interferometers, such as the Space Interferometer Mission Planet Quest (SIM), require thermal stability of the optical wavefront to the level of picometers in order to produce astrometric data at the micro-arc-second level. In SIM, the internal path of the interferometer will be measured with a small metrology beam whereas the starlight fringe position is estimated from a large concentric annular beam. To achieve the micro-arc-second observation goal for SIM, it is necessary to maintain the optical path difference between the central and the outer annulus portions of the wavefront of the front-end telescope optics to a few tens of picometers. The Thermo-Opto-Mecha nical testbed (TOM3) was developed at the Jet Propulsion Laboratory to measure thermally induced optical deformations of a full-size flight-like beam compressor and siderostat, the two largest optics on SIM, in flight-like thermal environments. A Common Path Heterodyne Interferometer (COPHI) developed at JPL was used for the fine optical path difference measurement as the metrology sensor. The system was integrated inside a large vacuum chamber in order to mitigate the atmospheric and thermal disturbances. The siderostat was installed in a temperature-controlled thermal shroud inside the vacuum chamber, creating a flight-like thermal environment. Detailed thermal and structural models of the test articles (siderostat and compressor) were also developed for model prediction and correlation of the thermal deformations. Experimental data shows SIM required thermal stability of the test articles and good agreement with the model predictions.

interferometry↗
NASA NTRS2006

SIMsim: An End-to-end Simulator for the SIM Mission

In this paper we discuss the use of an innovative SIM simulator, called SIMsim, to perform end-to end simulations of the SIM mission. The inputs to the simulator are a physically-based parameterization of the major SIM error sources and the output is the mission astrometric accuracy for various observing scenarios such as narrow-angle (NA) and wide-angle (WA) observations. The primary role of SIMsim is to validate the SIM astrometric error budget (AEB), bit it is also being used to study a variety of mission performance issues as well as being a test-bed for prototype data reduction algorithms. SIMsim is giving us confidence that the SIM AEB is a valid estimate of mission performance. It also is illustrating where analytical formulas for estimating certain effects breakdown and a numerical approach has to be adopted.

sumulation↗
DOE OSTI2021

Review of WEC-Sim Development and Applications

WEC-Sim (Wave Energy Converter Simulator) is an open-source code for simulating wave energy converters that has been actively developed and applied to simulate a wide variety of device archetypes, and has become a popular tool since its release. This paper reviews the development efforts and usage of WEC-Sim. The publications considered in this study have been broken down into six topic areas, namely, feature development, experimental validation, device modelling, control modelling, powertake-off (PTO) and grid modelling, and novel applications, which includes some non-wave energy applications. This review paper also recognizes the contributions of academic researchers and technology developers from around the world toward the broader WEC-Sim development effort. The growing number of external applications of WEC-Sim demonstrates a broader acceptance of the open-source code, and the ways WEC-Sim has been used in certain topic areas also highlight potential future development needs.

applications↗
DOE OSTI2020

Secondary Ion Mass Spectrometry (SIMS) for Chemical Characterization of Metal Halide Perovskites

Metal halide perovskite (MHP) solar cells have attracted much attention due to the rapidly growing power conversion efficiency that has reached 25.2% in a decade, comparable to established commercial photovoltaic modules. Compositional engineering is one of the most effective methods to boost the performance of MHP solar cells. Further improving the efficiency and the stability of MHP solar cells necessitates good understanding of the chemical–efficiency correlation and the chemical evolution during the degradation of MHP solar cells. In this regard, time-of-flight secondary ion mass spectrometry (ToF-SIMS) is a powerful tool to investigate the chemical aspect of MHPs and has played an important role in advancing the development of MHP optoelectronics. However, up to date, a review that can guide future utilization of ToF-SIMS in the MHP development is missing. In this paper, the capabilities of ToF-SIMS in MHP investigations are summarized and analyzed from simple material synthesis and chemical distribution to more complicated device operation mechanism and stability. The strength of ToF-SIMS in resolving important issues in this field, such as interface composition, ion migration, and degradation in MHP is highlighted. Finally, an outlook with an emphasis on making the utmost of ToF-SIMS in developing MHP devices is provided.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Nanoscale imaging of hydrogen and sodium in alteration layers of corroded glass using ToF-SIMS: Is an auxiliary sputtering ion beam necessary?

The hydrogen (H)/sodium (Na) interface is of great interest in glass corrosion research. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is one of the few techniques that can provide nanoscale H and Na imaging simultaneously. However, the optimized condition for ToF-SIMS imaging of H in glass is still unclear. In H depth profiling using ToF-SIMS, H background control is a key, in which an analysis ion beam and a sputtering ion beam work together in an interlaced mode to minimize it. Therefore, it is of great interest to determine if an auxiliary sputtering ion beam is also necessary to control H background in ToF-SIMS imaging of H. In this study, a Bi+ primary ion beam with different auxiliary sputtering beams (Cs+, O2+ and Arn+) were compared on a corroded International Simple Glass (ISG). It was surprising that the H/Na interface could be directly imaged using positive ion imaging without any auxiliary sputtering ion beam under a vacuum of 2-3 × 10-8 mbar. The H+ background was about 5% atomic percent on the pristine ISG glass, which was significantly lower than the H concentration in the alteration layer (~15%). Moreover, positive ion imaging could show distributions of other interesting species simultaneously, providing more comprehensive information of the glass corrosion. The H+ background could be reduced with an auxiliary O2+ sputtering ion beam; however, significant loss of signal intensities was observed. In addition, a higher H background in ToF-SIMS imaging than that in the depth profiling was observed.

Zhang, Jiandong↗
DOE OSTI2017

Graphene Oxide as a Novel Evenly Continuous Phase Matrix for TOF-SIMS

Using matrix to enhance the molecular ion signals for biomolecule identification without loss of spatial resolution caused by matrix crystallization is a great challenge for the application of TOF-SIMS in real-world biological research. In this report, graphene oxide (GO) was used as a matrix for TOF-SIMS to improve the secondary ion yields of intact molecular ions ([M + H]{sup +}). Identifying and distinguishing the molecular ions of lipids (m/z >700) therefore became straightforward. The spatial resolution of TOF-SIMS imaging could also be improved as GO can form a homogeneous layer of matrix instead of crystalline domain, which prevents high spatial resolution in TOF-SIMS imaging. Lipid mapping in presence of GO revealed the delicate morphology and distribution of single vesicles with a diameter of 800 nm. On GO matrix, the vesicles with similar shape but different chemical composition could be distinguished using molecular ions. This novel matrix holds potentials in such applications as the analysis and imaging of complex biological samples by TOF-SIMS. .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Machine Learning Correlation of Electron Micrographs and ToF-SIMS for the Analysis of Organic Biomarkers in Mudstone

The spatial distribution of organics in geological samples can be used to determine when and how these organics were incorporated into the host rock. Mass spectrometry (MS) imaging can rapidly collect a large amount of data, but ions produced are mixed without discrimination, resulting in complex mass spectra that can be difficult to interpret. Here, we apply unsupervised and supervised machine learning (ML) to help interpret spectra from time-of-flight-secondary ion mass spectrometry (ToF-SIMS) of an organic-carbon-rich mudstone of the Middle Jurassic of England (UK). It was previously shown that the presence of sterane molecular biomarkers in this sample can be detected via ToF-SIMS (Pasterski, M. J. et al., Astrobiology 2023, 23, 936). We use unsupervised ML on scanning electron microscopy–electron dispersive spectroscopy (SEM-EDS) measurements to define compositional categories based on differences in elemental abundances. We then test the ability of four ML algorithms─k-nearest neighbors (KNN), recursive partitioning and regressive trees (RPART), eXtreme gradient boost (XGBoost), and random forest (RF)─to classify the ToF-SIM spectra using (1) the categories assigned via SEM-EDS, (2) organic and inorganic labels assigned via SEM-EDS, and (3) the presence or absence of detectable steranes in ToF-SIMS spectra. In terms of predictive accuracy and balanced accuracy, KNN was the best performing model and RPART the worst. The feature importance, or the specific features of the ToF-SIM spectra used by the models to make classifications, cannot be determined for KNN, preventing posthoc model interpretation. Nevertheless, the feature importance extracted from the other models was useful for interpreting spectra. In conclusion, we determined that some of the organic ions used to classify biomarker containing spectra may be fragment ions derived from kerogen which is abundant in this mudstone sample.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Sim-Situ: A Framework for the Faithful Simulation of in situ Processing

The amount of data generated by numerical simulations in various scientific domains led to a fundamental redesign of how the analysis and visualization of simulation outputs are performed. The throughput and capacity of storage subsystems have not evolved as fast as the computing power in extreme-scale supercomputers, making the classical post-hoc approach highly inefficient. In situ processing has then emerged as a solution in which simulation and data analysis/visualization are intertwined for better performance and greater interactivity.Determining the best allocation, i.e., how many resources to allocate to simulation and analysis respectively, mapping, i.e., where and at which frequency to run the analysis/visualization, and data transfer mode is a complex task whose performance assessment is crucial to the efficient execution of in situ processing. However, such a performance evaluation of different strategies usually relies either on directly running them on the targeted execution environments, which can rapidly become extremely time- and resource-consuming, or on resorting to simplified models of the components of an in situ application, which can lack of realism. In both cases, the validity of the performance evaluation is limited.In this paper, we present Sim-Situ, a simulation-based framework for the faithful performance evaluation of in situ processing strategies. We designed Sim-Situ to reflect the typical features of in situ processing systems. Thanks to its modular design, Sim-situ has the necessary flexibility to easily and faithfully evaluate the behavior and performance of various allocation, mapping, and data transfer strategies. We illustrate the simulation capabilities of Sim-Situ on a Molecular Dynamics use case. We study the impact of different strategies on performance and show how users can leverage Sim-Situ to determine interesting tradeoffs when adding analysis/visualization components to their application.

Honoré, Valentin↗