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Results for “in situ visualization”
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Towards elastic in situ analysis for high-performance computing simulations
In situ analysis and visualization have grown increasingly popular for enabling direct access to data from high-performance computing (HPC) simulations. As a simulation progresses and interesting physical phenomena emerge, however, the data produced may become increasingly complex, and users may need to dynamically change the type and scale of in situ analysis tasks being carried out and consequently adapt the amount of resources allocated to such tasks. To date, none of the production in situ analysis frameworks offer such an elasticity feature, and for good reason: the assumption that the number of processes could vary during run time would force developers to rethink software and algorithms at every level of the in situ analysis stack. In this paper we present Colza, a data staging service with elastic in situ visualization capabilities. We demonstrate the use of Colza with the Deep Water Impact and the AMR-Wind simulations, coupling them with the ParaView Catalyst and Ascent in situ libraries, and show that Colza enables dynamic rescaling of these widely-used frameworks with no interruption to the simulation or staging service. Here, we highlight the challenges of enabling such elasticity, which requires overcoming these frameworks' reliance on MPI, using distinct engineering approaches, namely dependency injection and dependency overload. To the best of our knowledge, this work is the first to enable elastic in situ visualization capabilities for HPC applications on top of existing production analysis tools.
Simultaneous neutron and X-ray tomography for visualization of graphite electrode degradation in fast-charged lithium-ion batteries
Advanced battery characterization using neutron and X-ray-based imaging modalities is crucial to reveal fundamental degradation modes of lithium-ion batteries (LIBs). Taking advantage of the sensitivity of neutrons to some low-Z (Li) and X-rays to high-Z materials (Cu), here we demonstrate the viability of simultaneous neutron and X-ray tomography (NeXT) as a non-destructive imaging platform for ex-situ 3D visualization of graphite electrode degradation following extreme fast charging (XFC). In addition, we underscore the benefits of the simultaneous of NeXT by combining the neutron and X-ray tomography data from the same sample location for material identification and segmentation of one pristine and two XFC-cycled graphite electrodes (9C charge for 450 cycles). Our ex-situ results and methodology development pave the way for the design of NeXT-friendly LIB geometries that will allow operando and/or in-situ 3D visualization of electrode degradation during XFC.
Visualization of in-situ chemical flow through sand using neutron radiography
Chemical movement through soil is an important process in agriculture and ecology. Observing the spatial and temporal dynamics of these processes using conventional chemical ecology methods requires techniques that are destructive and/or lack resolution. Neutron radiography has the capability to allow chemical motion through sand/soil to be tracked with high spatial and temporal resolution, and we show that it allows for the motion of hydrophobic and hydrophilic chemicals to be distinguished. This technique can have an important impact on introducing neutron radiography to a wider community and into our understanding of chemical communication dynamics between plants and movement of applied chemicals in agricultural soils.
In-Situ Partial Pressure Measurements and Visual Observation during Crystal Growth of ZnSe by Seeded Physical Vapor Transport
An in-situ monitoring furnace was constructed with side windows to perform partial pressure measurements by optical absorption and visual observation of the growing crystal. A fused silica -rowth ampoule with a 4.5 cm long square tube between the source and the seed was prepared for the optical absorption measurements. A ZnSe crystal was grown by the seeded physical vapor transport (PVT) technique in the horizontal configuration. The growth temperature was 1120 C and the furnace translation rate was 3nmVday. Partial pressures of Se2, P(sub Se2), at three locations along the length of the growth ampoule were measured at 90 min intervals during the growth process. The measured P (sub Se2) were in the range of 2.0 to 6.5 x 10(exp -3) atm. The P(sub Se2) results indicated that the partial pressure profile was inconsistent with the results of the one-dimensional diffusion mass transport model and that the source composition shifted toward Se-rich during the run, i.e. the grown crystal was more Zn-rich than the source. The visual observation showed that the seed crystal first etched back, with greater thermal etching occurring along the edges of the seed crystal. Once the growth started, the crystal crew in a predominately contactless mode and facets were evident during growth. The crystal did not grow symmetrically which is believed to be due to the unintentional asymmetry of the radial thermal profile in the furnace.
In situ multimodal imaging for nanoscale visualization of tribofilm formation
A third of the energy from fuel combustion in passenger car gasoline engines is lost due to friction. Carefully designed engine lubricants can recover some of these losses by reducing friction and wear by forming a nanometer-scale chemico-physico tribofilm between surfaces. Accordingly, attention has focused on developing oil formulations that form low-friction tribofilms. However, analyses of resultant tribofilms are typically conducted after tribo-tests with conventional characterization tools and do not offer insights into tribofilm formation and evolution, precluding information critical to tuning tribofilm properties. In this work, we developed a unique multimodal methodology based on Atomic Force Microscopy (AFM) with local probe heating for in situ tribological studies that activates friction modifiers and simultaneously captures the evolution of friction and surface roughness, with nanometer resolution. As a platform to demonstrate the ability of this methodology to visualize dynamics of tribofilm formation in situ, we apply it to molybdenum-based friction modifiers to distinguish key factors in their functionality and correlate nanoscale AFM and Friction Force Microscopy data to bench tribo-tests used in the industry. To decode the formation mechanisms observed in situ and underlying chemistry of tribofilms, we performed ab initio Molecular Dynamics (AIMD) simulations at comparable conditions. AIMD simulations confirmed both nanoscale and bench tribo-test results and showed deviations in molecular organization in tribofilms that are formed from different molybdenum-based friction modifiers that corroborates with surface functionality. With this innovative methodology, we demonstrate proof-of-principle in situ formation of molybdenum-based tribofilms directly on steel surfaces that could be applied generally to studying tribofilm formation.
In-situ X-ray and visual observation of foam morphology and behavior at the batch-melt interface during melting of simulated waste glass
We report to attain a basic understanding of the primary foam structure and behavior, which affects the heat and mass transfer and the efficiency of the glass melting process, we investigated the primary foam layer under the glass batch floating on molten glass. The primary foam affects mass transfer during batch melting, in turn affecting the melting process. The recently performed direct in-situ three-dimensional X-ray computed tomography of the batch melting in a laboratory-scale melter vessel allowed us to visualize the features of the reacting batch layer and the foam that develops at its bottom, though with an insufficient resolution of images. In this study, we obtained better temporal and spatial resolution using the two-dimensional X-ray radiography and visual observation of the structure and behavior of transient primary foam as it formed and decayed. As soon as the batch was charged onto the melt surface, foam bubbles began to evolve, grow, and coalesce, forming a primary foam layer, 5-10 mm thick, within tens of seconds. This foam layer was sustained by ongoing gas evolving reactions counterbalanced by bubble coalescence into cavities that moved sideways and escaped to the atmosphere. Eventually, the entire remaining batch turned into foam that gradually decayed at the melt surface. The decay rate agreed with literature observations of surface foam produced by secondary foaming.
Methodology of Atomic Force Microscopy Visualization of Electrode–Electrolyte Interfaces
Electrochemical atomic force microscopy (EC-AFM) provides unprecedented insights into the microstructure of electrode–electrolyte interfaces during electrochemical reactions. However, performing EC-AFM measurements has many challenges, for example, drift, contamination, and probe degradation. We present solutions to these experimental issues through electrochemical cell design and carefully chosen experimental parameters. The possibility that the probes can react with the interface during scanning, generating false-positive electrochemical dynamics, is discussed as an example of the challenge of high-fidelity EC-AFM measurement. Here, we demonstrate this effect in highly ordered pyrolytic graphite and show that we could use electrochemical control of the AFM probe to enable high-fidelity in situ AFM visualization of solid–liquid interfaces during electrochemical reactions.
Time-resolved 3D imaging of two-phase fluid flow inside a steel fuel injector using synchrotron X-ray tomography
The multiphase flow inside a diesel injection nozzle is imaged using synchrotron X-rays from the Advanced Photon Source at Argonne National Laboratory. Through acquisitions performed at several viewing angles and subsequent tomographic reconstruction, in-situ 3D visualization is achieved for the first time inside a steel injector at engine-like operating conditions. The morphology of the internal flow reveals strong flow separation and vapor-filled cavities (cavitation), the degree of which correlates with the nozzle's asymmetric inlet corner profile. Micron-scale surface features, which are artifacts of manufacturing, are shown to influence the morphology of the resulting liquid-gas interface. The data obtained at 0.1 ms time resolution exposes transient flow features and the flow development timescales are shown to be correlated with in-situ imaging of the fuel injector's hydraulically-actuated valve (needle). As more than 98.5% of the X-ray photon flux is attenuated within the steel injector body itself, we are posed with a unique challenge for imaging the flow within. Time-resolved imaging under these low-light conditions is achieved by exploiting both the refractive and absorptive properties of X-ray photons. The data-processing strategy converted these images with a signal-to-noise ratio of similar to 10 into a meaningful dataset for understanding internal flow and cavitation in a nozzle of diameter 200 mu m enclosed within 1-2 millimeters of steel.
A simple convertible electrolyzer in membraneless and membrane-based modes for understanding water splitting mechanism
State-of-the-art membrane-based electrolyzers such as proton exchange membrane electrolyzer cells, are costly, susceptible to degradation, and time-consuming for electrode evaluation and triple-phase boundary electrochemical reaction studies. Here, a simple convertible electrolyzer in membraneless and membrane-based modes is proposed. For the first time, this enables comprehensive investigations of water splitting with pure water, acidic and alkaline electrolytes in one cell. With the simple electrolyzer and high-speed visualization system, the influences of flow rate, electrolytes, concentration, and Nafion membrane on the oxygen evolution reactions (OERs), hydrogen evolution reactions (HERs) and electrolyzer performance are comprehensively investigated. Visualization results reveal that water splitting only occurred at the edge between the electrode and the Nafion membrane in pure water. However, they occurred on the whole electrode surface in alkaline and acidic electrolytes, indicating easily tunable reaction sites with the convertible electrolyzer. This demonstrates the feasibility of using the simple convertible electrolyzer for understanding the water splitting mechanism. The relation between electrolyte thickness and resistances with different electrolytes is also quantified. This research provides an insight for optimizing electrochemical devices while delivering an inexpensive and fast way for electrode evaluations and electrochemical reaction studies.
Peptoid-Loaded Microgels Self-Defensively Inhibit Staphylococcal Colonization of Titanium in a Model of Operating-Room Contamination
Bacterial contamination of an exposed implantable medical device by the atmosphere of an operating room (OR) is increasingly implicated as a cause of device-associated infection. Here, OR contamination is modeled in vitro using an aerosolizing system to spray small quantities of staphylococci onto titanium rods. Contaminated rods always manifest culturable bacteria. Self-assembly is used to create a self-defensive Ti surface that substantially enhances the rod's resistance to such contamination. Poly(acrylic acid) microgels are electrostatically deposited onto small Ti rods and subsequently loaded by complexation with a cationic antimicrobial peptoid (TM1). The microgels are visualized in situ by optical microscopy, and changes in microgel diameter indicate the loading state. Further, these measurements show that TM1 can be quickly loaded from low-ionic-strength buffer and subsequently remained sequestered within the microgels for up to 4 weeks when soaked in phosphate buffered saline. TM1-loaded microgel-modified Ti surfaces are contaminated with aerosolized staphylococci, and subsequent assays indicate few or no culturable bacteria. In the absence of nutrients to enable metabolism, this finding suggests that bacteria trigger local TM1 release by contact transfer. The modified surfaces exhibit good in vitro cytocompatibility as manifested by the adhesion, spreading, and metabolic activity of human fetal osteoblasts.
Laboratory-Based Micro-X-ray Computed Tomography of Energy Materials at Idaho National Laboratory
Abstract The Idaho National Laboratory (INL) has implemented laboratory-based micro-X-ray computed tomography in a laboratory equipped for the examination of highly radioactive samples. This capability provides nondestructive three-dimensional volumetric information on samples to inform subsequent traditional destructive examinations as well as real-world inputs for high-fidelity scientific modeling. Samples can be imaged with spatial resolutions ranging from several hundred nm/voxel up to ~ 100 µm/voxel. The best usable spatial resolution achieved to date is 384 nm/voxel with this instrument, while the highest radiological dose rate of a sample imaged is ~ 60 R/h β/γ on contact. Advanced data analysis, including custom tomographic reconstruction and segmentation methods, have also been developed to support this capability. In addition to traditional digital X-ray radiography and tomography, this instrument is also able to visualize in situ tensile and compression testing as well as perform diffraction contrast tomography. This work describes the X-ray computed tomography post-irradiation examination capabilities at INL, as well as detailing a variety of applications this instrument has examined.
Serendipita indica Drives Sulfur-Related Microbiota in Enhancing Growth of Hyperaccumulator Sedum alfredii and Facilitating Soil Cadmium Remediation
Endophytic fungus Serendipita indica can bolster plant growth and confer protection against various biotic and abiotic stresses. However, S. indica -reshaped rhizosphere microecology interactions and root-soil interface processes in situ at the submicrometer scale remain poorly understood. Here, we combined amplicon sequencing and high-resolution nano X-ray fluorescence (nano-XRF) imaging of the root-soil interface to reveal cadmium (Cd) rhizosphere processes. S. indica can successfully colonize the roots of Sedum alfredii Hance, which induces a remarkable increase in shoot biomass by 211.32% and Cd accumulation by 235.72%. Nano-XRF images showed that S. indica colonization altered the Cd distribution in the rhizosphere and facilitated the proximity of more Cd and sulfur (S) to enter the roots and transport to the shoot. Furthermore, the rhizosphere-enriched microbiota demonstrated a more stable network structure after the S. indica inoculation. Keystone species were strongly associated with growth promotion and Cd absorption. For example, Comamonadaceae are closely related to the organic acid cycle and S bioavailability, which could facilitate Cd and S accumulation in plants. Meanwhile, Sphingomonadaceae could release auxin and boost plant biomass. In summary, we construct a mutualism system for beneficial fungi and hyperaccumulation plants, which facilitates high-efficient remediation of Cd-contaminated soils by restructuring the rhizosphere microbiota.
High-temperature high-pressure microfluidic system for rapid screening of supercritical CO 2 foaming agents
CO 2 foam helps to increase the viscosity of CO 2 flood fluid and thus improve the process efficiency of the anthropogenic greenhouse gas’s subsurface utilization and sequestration. Successful CO 2 foam formation mandates the development of high-performance chemicals at close to reservoir conditions, which in turn requires extensive laboratory tests and evaluations. This work demonstrates the utilization of a microfluidic reservoir analogue for rapid evaluation and screening of commercial surfactants (i.e., Cocamidopropyl Hydroxysultaine, Lauramidopropyl Betaine, Tallow Amine Ethoxylate, N,N,N' Trimethyl-N'-Tallow-1,3-diaminopropane, and Sodium Alpha Olefin Sulfonate) based on their performance to produce supercritical CO 2 foam at high salinity, temperature, and pressure conditions. The microfluidic analogue was designed to represent the pore sizes of the geologic reservoir rock and to operate at 100 °C and 13.8 MPa. Values of the pressure drop across the microfluidic analogue during flow of the CO 2 foam through its pore network was used to evaluate the strength of the generated foam and utilized only milliliters of liquid. The transparent microfluidic pore network allows in-situ quantitative visualization of CO 2 foam to calculate its half-life under static conditions while observing if there is any damage to the pore network due to precipitation and blockage. The microfluidic mobility reduction results agree with those of foam loop rheometer measurements, however, the microfluidic approach provided more accurate foam stability data to differentiate the foaming agent as compared with conventional balk testing. The results obtained here supports the utility of microfluidic systems for rapid screening of chemicals for carbon sequestration or enhanced oil recovery operations.
Stomata in-sight: Integrating live confocal microscopy with leaf gas exchange and environmental control
Stomatal anatomy (aperture area, length, and width) influences leaf-level physiology traits including conductance to water vapor. Stomatal anatomy can be visualized in situ by microscopy, but the difficulty of regulating the atmospheric environment of a microscope stage means that the conditions under which imaging is done are rarely physiologically relevant. Alternatively, leaf gas exchange instruments that measure gas fluxes reflect stomatal anatomical characteristics in aggregate, but the relative strengths of anatomical traits to control water use (e.g. size vs density) cannot be firmly established. To reconcile the microscopic stomatal characteristics with leaf-level gas exchange, we describe a tool that combines laser scanning confocal microscopy, gas exchange instruments, and machine-learning image analysis to simultaneously observe anatomical characteristics of many (>40) stomata alongside leaf-level traits like photosynthesis, transpiration, and stomatal conductance. We demonstrate how the tool has the resolution capable of quantifying aperture sizes and variability in maize (Zea mays) leaves under 5 steady-state light/pCO 2 treatments while tightly controlling other environmental variables like relative humidity and temperature. A model used to calculate stomatal conductance from measured apertures and stomatal density accurately matched stomatal conductance measured by gas exchange. This technical advancement will provide insight on how stomatal anatomy and function trade off to influence stomatal conductance and leaf-level water use efficiency.
Capturing Carbonation: Understanding Kinetic Complexities through a New Era of Electron Microscopy
Cryogenic plasma focused ion beam (PFIB) electron microscopy analysis is applied to visualizing ex situ (surface industrial) and in situ (subsurface geologic) carbonation products, to advance understanding of carbonation kinetics. Ex situ carbonation is investigated using NIST fly ash standard #2689 exposed to aqueous sodium bicarbonate solutions for brief periods of time. In situ carbonation pathways are investigated using volcanic flood basalt samples from Schaef et al. (2010) exposed to aqueous CO 2 solutions by them. The fly ash reaction products at room temperature show small amounts of incipient carbonation, with calcite apparently forming via surface nucleation. Reaction products at 75° C show beginning stages of an iron carbonate phase, e.g., siderite or ankerite, common phases in subsurface carbon sequestration environments. This may suggest an alternative to calcite in carbonation low calcium-bearing fly ashes. Flood basalt carbonation reactions show distinct zonation with high calcium and calcium-magnesium bearing zones alternating with high iron-bearing zones. The calcium-magnesium zones are notable with occurrence of localized pore space. Oscillatory zoning in carbonate minerals is distinctly associated with far-from-equilibrium conditions where local chemical environments fluctuate via a coupling of reaction with transport. The high porosity zones may reflect a precursor phase (e.g., aragonite) with higher molar volume that then “ripens” to the high-Mg calcite phase-plus-porosity. These observations reveal that carbonation can proceed with evolving local chemical environments, formation and disappearance of metastable phases, and evolving reactive surface areas. Together this work shows that future application of cryo-PFIB in carbonation studies would provide advanced understanding of kinetic mechanisms for optimizing industrial-scale and commercial-scale applications.
Induced microearthquakes predict permeability creation in the brittle crust
Predicting the evolution of permeability accurately during stimulation at the reservoir scale and at the resolution of individual fractures is essential to characterize the fluid transport and the reactive/heat-transfer characteristics of reservoirs where stress exerts significant control. Here, we develop a hybrid machine learning (ML) model to visualize in situ permeability evolution for an intermediate-scale (~10 m) hydraulic stimulation experiment. This model includes an ML model that was trained using the well history of flow rate and wellhead pressure and MEQ data from the first three stimulation episodes to predict average permeability from the statistical features of the MEQs alone for later episodes. Moreover, a physics-inspired model is integrated to estimate in situ fracture permeability spatially. This method relates fracture permeability to fracture dilation and scales dilation to the equivalent MEQ magnitude, according to laboratory observations. The seismic data are then applied to define incremental changes in permeability in both space and time. Our results confirm the excellent agreement between the ground truth and model-predicted permeability evolution. The resulting permeability map defines and quantifies flow paths in the reservoir with the averaged permeability comparing favorably with the ground truth of permeability.
Production of RNA by a polymerase protein encapsulated within phospholipid vesicles
Catalyzed polymerization reactions represent a primary anabolic activity of all cells. It can be assumed that early cells carried out such reactions, in which macromolecular catalysts were encapsulated within some type of boundary membrane. In the experiments described here, we show that a template-independent RNA polymerase (polynucleotide phosphorylase) can be encapsulated in dimyristoyl phosphatidylcholine vesicles without substrate. When the substrate adenosine diphosphate (ADP) was provided externally, long-chain RNA polymers were synthesized within the vesicles. Substrate flux was maximized by maintaining the vesicles at the phase transition temperature of the component lipid. A protease was introduced externally as an additional control. Free enzyme was inactivated under identical conditions. RNA products were visualized in situ by ethidium bromide fluorescence. The products were harvested from the liposomes, radiolabeled, and analyzed by polyacrylamide gel electrophoresis. Encapsulated catalysts represent a model for primitive cellular systems in which an RNA polymerase was entrapped within a protected microenvironment.