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At least 451 records · Page 25

Lambda-PFLOTRAN 1.0: a workflow for incorporating organic matter chemistry informed by ultra high resolution mass spectrometry into biogeochemical modeling

Abstract. Organic matter (OM) composition plays a central role in microbial respiration of dissolved organic matter and subsequent biogeochemical reactions. Here, a direct connection of organic matter chemistry and thermodynamics to reactive transport simulators has been achieved through the newly developed Lambda-PFLOTRAN workflow tool that succinctly incorporates carbon chemistry data generated from Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) into reaction networks to simulate organic matter degradation and the resulting biogeochemistry. Lambda-PFLOTRAN is a Python-based workflow, executed through a Jupyter notebook interface, that digests raw FTICR-MS data, develops a representative reaction network based on substrate-explicit thermodynamic modeling (also termed lambda modeling due to its key thermodynamic parameter λ used therein), and completes a biogeochemical simulation with the open source, reactive flow and transport code PFLOTRAN. The workflow consists of the following five steps: configuration, thermodynamic (lambda) analysis, sensitivity analysis, parameter estimation, and simulation output and visualization. Two test cases are provided to demonstrate the functionality of the Lambda-PFLOTRAN workflow. The first test case uses laboratory incubation data of temporal oxygen depletion to fit lambda parameters (i.e., maximum utilization rate and microbial carrying capacity). A slightly more complex second test case fits multiple lambda formulation and soil organic matter release parameters to temporal greenhouse gas generation measured during a soil incubation. Overall, the Lambda-PFLOTRAN workflow facilitates upscaling by using molecular-scale characterization to inform biogeochemical processes occurring at larger scales.

58 GEOSCIENCES↗

On the structure of the drifton phase space and its relation to the Rayleigh–Kuo criterion of the zonal-flow stability

The phase space of driftons (drift-wave quanta) is studied within the generalized Hasegawa–Mima collisionless-plasma model in the presence of zonal flows. This phase space is made intricate by the corrections to the drifton ray equations that were recently proposed by Parker [J. Plasma Phys. 82, 595820602 (2016)] and Ruiz et al. [Phys. Plasmas 23, 122304 (2016)]. Contrary to the traditional geometrical-optics (GO) model of the drifton dynamics, it is found that driftons can not only be trapped or passing but also accumulate spatially while experiencing indefinite growth of their momenta. In particular, it is found that the Rayleigh–Kuo threshold known from geophysics corresponds to the regime when such “runaway” trajectories are the only ones possible. On one hand, this analysis helps to visualize the development of the zonostrophic instability, particularly its nonlinear stage, which is studied here both analytically and through wave-kinetic simulations. On the other hand, the GO theory predicts that zonal flows above the Rayleigh–Kuo threshold can only grow; hence, the deterioration of intense zonal flows cannot be captured within a GO model. In particular, this means that the so-called tertiary instability of intense zonal flows cannot be adequately described within the quasilinear wave kinetic equation, contrary to some previous studies.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

OH PLIF Visualization of an Optically Accessible Rotating Detonation Combustor

OH PLIF imaging has been successfully conducted within an optically accessible race- track shaped rotating detonation combustor. The OH PLIF images taken in this study corroborate the overall flow field structure reconstructed from previous OH* chemilumi- nescence studies conducted on the same combustor. However, the increased spatial and temporal resolution achieved with the OH PLIF technique allowed for the identification of previously unknown structures present in the detonation wave and its wake. These struc- tures appear as non-uniformities in the OH PLIF signal throughout the channel. Smaller scale structures range from variations in light intensity all the way to seemingly unburnt gas pockets passing through the detonation wave, suggesting non uniform reaction across the propagating detonation wave. Also present in the flow is a relatively large structure, consisting of a dark band surrounded by regions of higher OH intensity that trails the detonation wave. This band is hypothesized to be a result of the effect of secondary waves on the injection system and subsequent fill region composition stratification. Both of these flow structures represent potential avenues for performance loss through off-design mixing and heat release being uncoupled from the detonation wave.

Chacon, Fabian↗

In-situ tube burst testing and high-temperature deformation behavior of candidate materials for accident tolerant fuel cladding

The high resistance of cladding to plastic deformation and burst failure is one of the most essential properties of accident tolerant fuel (ATF) for maintaining structural integrity during a loss-of-coolant accident (LOCA) since the deformation and burst behavior governs the cooling efficiency of flow channels and process of fission product release. To simulate and evaluate such deformation and burst process of thin-walled cladding, an in-situ testing and evaluation method has been developed on the basis of visual imaging and image analysis techniques. The method uses a specialized optics system consisted of a high-resolution video camera, light filtering unit, and monochromatic light sources, and the in-situ testing is performed using a 50 mm long pressurized thin-walled tubular specimen set in a programmable furnace. In this study eleven (11) candidate cladding materials for ATF, i.e., 6 FeCrAl alloys and 5 nanostructured steels, were tested using the newly developed method, and the time-dependent images were analyzed to produce detailed deformation and burst data such as true hoop stress, strain (creep) rate, and failure stress. Relatively soft FeCrAl alloys deformed and burst below 800°C while negligible strain rates were measured for higher strength alloys and/or for relatively thick wall specimens.

Gussev, Maxim N.↗

Nanoparticle Tracking to Probe Transport in Porous Media

From the granular and fractured subsurface environment to highly engineered polymer membranes used in pharmaceutical purification, porous materials are ubiquitous in nature and industrial applications. In particular, porous media are used extensively in processes including water treatment, pharmaceutical sterilization, food/beverage processing and heterogeneous catalysis, where hindered mass transport is either essential to the process or a necessary, but undesirable limitation. Unfortunately, there are currently no universal models capable of predicting mass transport based on a description of the porous material because real porous materials are complex, and because many coupled dynamic mechanisms (e.g. adsorption, steric effects, hydrodynamic effects, electrostatic interactions, etc.) give rise to the observed macroscopic transport phenomena. While classical techniques, like nuclear magnetic resonance and dynamic light scattering, provide useful information about mass transport in porous media at the ensemble level, they provide limited insight into the microscopic mechanisms that give rise to complex phenomena such as anomalous diffusion, hindered pore-space accessibility, and unexpected retention under flow, among many others. To address this issue, we have developed refractive index matching imaging systems, combined with single-particle tracking methods, allowing the direct visualization of single particle motion within a variety of porous materials. Here, we summarize our recent efforts to advance the understanding of nanoparticle transport in porous media using single-particle tracking methods in both fundamental and applied scenarios. First, we describe the basic principles for two-dimensional and three-dimensional single-particle tracking in porous materials. Then, we describe concrete examples of nanoparticle transport in porous materials from two perspectives: (1) understanding fundamental elementary particle transport processes in porous media, including pore accessibility and cavity escape, which limit transport in porous media; (2) facilitating applications in industrial processes, e.g. by understanding the mechanisms of particle fouling and remobilization in filtration membranes. Finally, we provide an outlook of opportunities associated with investigating other types of mass transport in confined environments using single-particle tracking methods, including electrophoretic and self-propelled motion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Nuflood, Version 1.x

Nuflood Version 1.x is a surface-water hydrodynamic package designed for the simulation of overland flow of fluids. It consists of various routines to address a wide range of applications (e.g., rainfall-runoff, tsunami, storm surge) and real time, interactive visualization tools. Nuflood has been designed for general-purpose computers and workstations containing multi-core processors and/or graphics processing units. The software is easy to use and extensible, constructed in mind for instructors, students, and practicing engineers. Nuflood is intended to assist the water resource community in planning against water-related natural disasters.

Tasseff, Byron↗

Monte Carlo Simulation and Reconstruction: Assessment of Myocardial Perfusion Imaging of Tracer Dynamics With Cardiac Motion Due to Deformation and Respiration Using Gamma Camera With Continuous Acquisition

Purpose: Myocardial perfusion imaging (MPI) with single photon emission computed tomography (SPECT) is routinely used for stress testing in nuclear medicine. Recently, our group extended its potential going from 3D visual qualitative image analysis to 4D spatiotemporal reconstruction of dynamically acquired data to capture the time variation of the radiotracer concentration and the estimated myocardial blood flow (MBF) and coronary flow reserve (CFR). However, the quality of reconstructed image is compromised due to cardiac deformation and respiration. The work presented here develops an algorithm that reconstructs the dynamic sequence of separate respiratory and cardiac phases and evaluates the algorithm with data simulated with a Monte Carlo simulation for the continuous image acquisition and processing with a slowly rotating SPECT camera. Methods: A clinically realistic Monte Carlo (MC) simulation is developed using the 4D Extended Cardiac Torso (XCAT) digital phantom with respiratory and cardiac motion to model continuous data acquisition of dynamic cardiac SPECT with slowly rotating gamma cameras by incorporating deformation and displacement of the myocardium due to cardiac and respiratory motion. We extended our previously developed 4D maximum-likelihood expectation-maximization (MLEM) reconstruction algorithm for a data set binned from a continuous list mode (LM) simulation with cardiac and respiratory information. Our spatiotemporal image reconstruction uses splines to explicitly model the temporal change of the tracer for each cardiac and respiratory gate that delineates the myocardial spatial position as the tracer washes in and out. Unlike in a fully list-mode data acquisition and reconstruction the accumulated photons are binned over a specific but very short time interval corresponding to each cardiac and respiratory gate. Reconstruction results are presented showing the dynamics of the tracer in the myocardium as it continuously deforms. These results are then compared with the conventional 4D spatiotemporal reconstruction method that models only the temporal changes of the tracer activity. Mean Stabilized Activity (MSA), signal to noise ratio (SNR) and Bias for the myocardium activities for three different target-to-background ratios (TBRs) are evaluated. Dynamic quantitative indices such as wash-in (K1) and wash-out (k2) rates at each gate were also estimated. Results: The MSA and SNR are higher with higher TBRs while biases were improved with higher TBRs to less than 10%. The correlation between exhalation-inhalation sequence with the ground truth during respiratory cycle was excellent. Our reconstruction method showed better resolved myocardial walls during diastole to systole as compared to the ungated 4D image. Estimated values of K1 and k2 were also consistent with the ground truth. Conclusion: The continuous image acquisition for dynamic scan using conventional two-head gamma cameras can provide valuable information for MPI. Our study demonstrated the viability of using a continuous image acquisition method on a widely used clinical two-head SPECT system. Our reconstruction method showed better resolved myocardial walls during diastole to systole as compared to the ungated 4D image. Precise implementation of reconstruction algorithms, better segmentation techniques by generating images of different tissue types and background activity would improve the feasibility of the method in real clinical environment.

60 APPLIED LIFE SCIENCES↗

Community Solar Project Models: An Introduction to Basic Financial and Administrative Relationships [Slides]

This resource is a collection of visual aids and descriptions to help explain the basic financial and administrative relationships underpinning common community solar project models. The graphics in this resource depict the flow of electricity from generation to consumption and the financial exchanges between the community solar project owner, subscribers, and distribution utility. Community solar models vary based on ownership (e.g., third party, utility), customer type (e.g., multifamily, single-household), and solar array location (e.g., on-site, off-site).

14 SOLAR ENERGY↗

High-speed characterization of two-phase flow and bubble dynamics in titanium felt porous media for hydrogen production

Bubble dynamics and two-phase flow phenomena are closely related to the performance of proton exchange membrane electrolyzer cells (PEMECs). This paper reports an in-situ study of the oxygen bubble behavior and associated multiphase evolutions in the anode side of PEMECs with titanium (Ti) felt liquid gas diffusion layers (LGDLs) by a high-speed visualization system. The micro oxygen bubble dynamics was captured and analyzed at different locations and virous operating conditions. The results show that the bubble detachment frequency and detachment diameter greatly increase with the operating current density. Additionally, they are significantly impacted by the local pore structure and morphology of Ti felt LGDLs. In the flow channels, there exist only several discrete micro bubbles at a low current density (0.04 A/cm 2 ) and a large flow velocity (133 mm/s). At a current density (0.2 A/cm 2 ) and a flow velocity (67 mm/s), a number of gas slugs are formed in the follow channels, in addition to discrete micro bubbles. At a high current density (1 A/cm 2 ) and a flow velocity (67 mm/s), more bubbles appear in the channel, and the flow field is dominated by slug or annular flows. These investigations can help to better understand the two-phase flow and bubble detachment mechanism, and provide a foundation for electrochemical reaction, multiphase flow studies and optimize the design of gas diffusion layers and flow fields for PEMECs in the future.

08 HYDROGEN↗

Dynamics of multilayer Rayleigh–Taylor instability at moderately high Atwood numbers

This paper investigates the multilayer Rayleigh–Taylor instability (RTI) using statistically stationary experiments conducted in a gas tunnel. Employing diagnostics such as particle image velocimetry (PIV) and planar laser induced fluorescence (PLIF), we make simultaneous velocity–density measurements to study how dynamics and mixing are linked in this variable density flow. Experiments are conducted in a newly built, blow-down three-layer gas tunnel facility. Mixing between three gas streams is studied, where the top and bottom streams are comprised of air, and the middle stream is an air–helium mixture. Shear is minimized between these streams by matching their inlet velocities. The four experimental conditions investigated here consist of two different density ratios (Atwood numbers 0.3 and 0.6), each investigated at two instability development times (or equivalently, two streamwise locations), and all experiments are with the same middle stream thickness of 3 cm. The growth of the middle layer is measured using laser-based planar Mie scattering visualization. The mixing width is found to grow linearly with time at late times. Various quantitative measures of molecular mixing indicate a very high degree of molecular mixing at late times in the multilayer RTI flow. The vertical turbulent mass flux $a_y$ is calculated. In addition to mostly negative values of $a_y$ , typical of buoyancy-dominated flows due to negative correlation between velocity and density fluctuations, positive regions are also observed in profiles of $a_y$ due to entrainment and erosion at the lower edge of the mixing region. Global energy budgets are calculated for the multilayer RTI flow at late times and it is found that the majority of potential energy released has been dissipated due to viscous effects, and a large value of mixing efficiency ( $\sim$ 60 %) is observed.

Mechanics↗

Laboratory Evaluation of a Natural Gas–Based Foamed Fracturing Fluid

Abstract Foams have been used as hydraulic fracturing fluids to reduce water usage and minimize the potentially deleterious impact on water-sensitive formations. Traditionally, carbon dioxide (CO2) and nitrogen (N2) have been used as the internal phase in these foamed fluids. Hydraulic fracturing with natural gas (NG) is a relatively inexpensive option, particularly if NG produced from the wellhead can be used without significant processing. In an ongoing program sponsored by the US Department of Energy (DOE), an alternative fracturing process is being developed that uses NG-based foam. Previously, the optimal thermodynamic pathway was identified to transform wellhead NG into pressurized NG suitable for use as the internal phase in a foamed fracturing fluid. Recent work has focused on preparing a NG-based foam at surface conditions typically encountered in hydraulic fracturing and measuring the stability and rheological properties of the foam. In addition, the transient response of the foam during fracture initiation was simulated using a fast-acting solenoid valve. A single base-fluid mixture was prepared by combining a commercially available viscosifier and foaming surfactant with water. The base fluid was then injected into a tee using a water pump. Simultaneously, liquefied natural gas (LNG) was pressurized using a cryogenic pump, vaporized using a heat exchanger, and injected into the tee to mix with the base fluid and generate foam. The foam then flowed through approximately 300 ft of 0.312-in. inside diameter (ID) tubing equipped with pressure transducers at several locations. The test fixture included a sight glass to visually inspect the quality of the foam. This paper reports on findings related to foam stability and rheology and compares these results to previous studies on foamed fracturing fluids.

Beck, Griffin↗

iMatTOUGH: An open-source Matlab-based graphical user interface for pre- and post-processing of TOUGH2 and iTOUGH2 models

TOUGH2 and iTOUGH2 are powerful models that simulate the heat and fluid flows in porous and fracture media, and perform parameter estimation, sensitivity analysis and uncertainty propagation analysis. However, setting up the input files is not only tedious, but error prone, and processing output files is time consuming. Here, we present an open source Matlab-based tool (iMatTOUGH) that supports the generation of all necessary inputs for both TOUGH2 and iTOUGH2 and visualize their outputs. The tool links the inputs of TOUGH2 and iTOUGH2, making sure the two input files are consistent. It supports the generation of rectangular computational mesh, i.e., it automatically generates the elements and connections as well as their properties as required by TOUGH2. The tool also allows the specification of initial and time-dependent boundary conditions for better subsurface heat and water flow simulations. The effectiveness of the tool is illustrated by an example that uses TOUGH2 and iTOUGH2 to estimate soil hydrological and thermal properties from soil temperature data and simulate the heat and water flows at the Rifle site in Colorado.

58 GEOSCIENCES↗

Coupled Transport, Reactivity, and Mechanics in Fractured Shale Caprocks

Abstract Shales are low‐permeability caprocks that confine fluid, such as CO 2 , nuclear waste, and hydrogen, in storage formations. Stress‐induced fractures in shale caprocks provide pathways for fluid to leak and potentially contaminate fresh water aquifers. Fractured shales are also increasingly considered as resources for CO 2 sequestration, enhanced geothermal, and unconventional energy recovery. Injecting reactive fluids into shales introduces chemical disequilibrium, causing an onset of a series of dissolution, precipitation, and fines mobilization mechanisms. The reactions have rapid kinetics and significant impact on porosity and permeability; consequently, flow and storage properties of caprocks. While previous research has explored the separate effects of these reactions, this study aims to uncover their simultaneous occurrence and collective influence. This study unveils these highly coupled transport and reactivity mechanisms by tracking and visualizing the reaction‐induced alterations in the matrix, microcracks, and fractures of shales over time. We conducted brine injection experiments sequentially at pH 4 and 2 in a naturally fractured Wolfcamp shale sample while simultaneously imaging the dynamic processes using X‐ray computed tomography (CT). CT images are validated by finer resolution images obtained using micro‐CT and scanning electron microscopy. We also tracked the sample permeability and fluid chemistry using brine permeability and inductively coupled plasma mass spectrometry, respectively. Findings show that fluid primarily flowed through fractures, dissolving reactive minerals and mobilizing fines on fracture surfaces. Dissolution of fracture asperities under confining stress resulted in the closing of fractures. Clogging in narrow fracture pathways, caused by fines accumulation, diverted fluid flow into matrix pores.

58 GEOSCIENCES↗

Small scale mechanical characterization of thin foil materials via pin load microtesting

In situ scanning electron microscope (SEM) experiments, where small-scale mechanical tests are conducted on micro- and nanosized specimens, allow direct visualization of elastic and plastic responses over the entirety of the volume being deformed. This enables precise spatial and temporal correlation of slip events contributing to the plastic flow evidenced in a stress–strain curve. A new pin-loading methodology has been employed, in situ within the SEM, to conduct microtensile tests on thin polycrystalline metal foils. This approach can be tailored to a specific foil whose particular grain size may range from microns to tens of microns. Manufacture of the specialized pin grip was accomplished via silicon photolithography-based processing followed by subsequent focused ion beam finishing. Microtensile specimen preparation was achieved by combining a stencil mask methodology employing broad ion beam sputtering along with focused ion beam milling in the study of several metallic foil materials. Finite-element analyses were performed to characterize the stress and strain distributions in the pin grip and micro-specimen under load. Furthermore, under appropriately conceived test conditions, uniaxial stress–strain responses measured within these foils by pin-load microtensile testing exhibit properties consistent with larger scale tests.

36 MATERIALS SCIENCE↗

Autophagy stimulated proliferation of porcine PSCs might be regulated by the canonical Wnt signaling pathway

Porcine pancreatic stem cells (PSCs) are one kind of the potential cells for treatment of human diabetes. Autophagy is a highly conserved cellular degradation process in which it helps to maintain the balance between the synthesis, degradation and subsequent recycling of cellular components. However, how autophagy contributes to PSCs has not yet been investigated. Here, we established GFP-LC3 transfected porcine PSC lines in which the accumulation of autophagosomes can be efficiently visualized to evaluate the autophagic activity. Moreover, we observed that starved PSCs which showed increased autophagic activity exhibited an increased tendency to proliferate through the results of BrdU, flow cytometry and western blotting. Furthermore, increased expression of active β-catenin after inducing autophagy indicated that it might be the canonical Wnt signaling that autophagy activated to exert the function on the stimulation of PSCs proliferation. Collectively, these results demonstrated that autophagy stimulated proliferation of PSCs might be regulated by the canonical Wnt signaling pathway. Our results for the first time shed light on a role of autophagy for stimulating the proliferation of porcine PSCs.

60 APPLIED LIFE SCIENCES↗

Merope: Unsupervised Learning for Network Operations (Merope) v1

The ability to analyze network flow characteristics is critical to understand network patterns that can help us understand how our networks are behaving. Merope is a collection of many unsupervised learning approaches and visualizers to allow networks to be more visual and analytical.

Kiran, Mariam↗

NEMA-Phase Compliant Traffic Signal Controller Module in SUMO

The controller modules in SUMO use a stage-based control structure. A phase is defined as a stage of all allowed movements at a time instance. However, traffic signal controllers used in North America widely use National Electrical Manufacturers Association (NEMA) phase definition. A NEMA phase is defined by a certain flow movement at an intersection. At one time, more than one NEMA phase could happen together as long as they do not conflict with each other. We can visualize the NEMA phases and timings in Ring-and-Barrier structured NEMA diagrams. For one controller, only one phase from a ring can be activated at a time. Phases from different rings could be activated together as long as they are not from the different sides of a barrier. When a controller is operated in fixed-time control mode, we can model the NEMA phase timing as a corresponding stage-based control timing without any issues. When introducing actuation into the signal control, a Ring-and-Barrier structured traffic signal controller can be more flexible than stage-based controller by allowing different possible phase combinations. We made two efforts in modeling Ring-and-Barrier structured controllers in SUMO. One is to translate a NEMA phases timing into SUMO-readable phases and timings as an additional file for SUMO. This translation worked well for fixed-time control. To model actuated control and coordinated actuated control, we augmented the SUMO source code by adding a Ring-and-Barrier structured controller module. This module could implement traffic signal timing from controllers using NEMA phases. We also augmented TraCI to be able to set new NEMA phase timings during simulations. We examined the Ring-and-Barrier structured traffic signal controller module by both visually observing the simulation animations and the simulation records. The developed control module can model the generalized Ring-and-Barrier structured traffic signal timing that is used in North America. SEE: https://github.com/eclipse/sumo/blob/main/src/microsim/traffic_lights/NEMAController.cpp

Wang, Qichao↗

Microbial Activity and Precipitation at Solution-Solution Mixing Zones in Porous Media -- Subsurface Biogeochemical Research

The goal for this research was to understand how best to add compounds to receptive microbial communities in porous media in order to achieve optimal calcite precipitation in a volumetrically significant space and to understand the physiological health of the cells that are responsible for the calcite precipitation. The specific objectives were to: (1) develop better tools for visually examining biofilms in porous media and calcium carbonate precipitation being mediated by microbes in porous media, and (2) demonstrate the effectiveness of using that tool within a flow cell model system.

54 ENVIRONMENTAL SCIENCES↗