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At least 55 records · Page 3

Lubricated immersed boundary method in two dimensions

Many biological examples of fluid-structure interaction, including the transit of red blood cells through the narrow slits in the spleen and the intracellular trafficking of vesicles into dendritic spines, involve the near-contact of elastic structures separated by thin layers of fluid. Motivated by such problems, we introduce an immersed boundary method that uses elements of lubrication theory to resolve thin fluid layers between immersed boundaries. We demonstrate 2nd-order accurate convergence for simple two-dimensional flows with known exact solutions to showcase the increased accuracy of this method compared to the standard immersed boundary method. Motivated by the phenomenon of wall-induced migration, we apply the lubricated immersed boundary method to simulate an elastic vesicle near a wall in shear flow. We also simulate the dynamics of a vesicle traveling through a narrow channel and observe the ability of the lubricated method to capture the vesicle motion on relatively coarse fluid grids.

59 BASIC BIOLOGICAL SCIENCES↗

Diffusion-driven Fluid Dynamics in Ideal Gases and Plasmas

The classical transport theory based on Chapman-Enskog methods provides self-consistent approximations for the kinetic flux of mass, heat, and momentum in a fluid limit characterized with a small Knudsen number. The species mass fluxes relative to the center of mass, or “diffusive fluxes,” are expressed as functions of known gradient quantities with kinetic coefficients evaluated using similar analyses for mixtures of gases or plasma components. The sum over species of the diffusive mass fluxes is constrained to be zero in the Lagrange frame, and thus results in a non-zero molar flux leading to a pressure perturbation. At an interface between two species initially in pressure equilibrium, the pressure perturbation driven by the diffusive molar flux induces a center of mass velocity directed from the species of greater atomic mass towards the lighter atomic mass species. As the ratio of the species particle masses increases, this center of mass velocity carries an increasingly greater portion of the mass across the interface and for a particle mass ratio greater than about two, the center of mass velocity carries more mass than the gradient driven diffusion flux. Early time transients across an interface between two species in a 1D plasma regime and initially in equilibrium are compared using three methods; a fluid code with closure in a classical transport approximation, a particle in cell simulation, and an implicit Fokker-Planck solver for the particle distribution functions. The early time transient phenomenology is shown to be similar in each of the computational simulation methods, including a pressure perturbation associated with the stationary “induced” component of the center of mass velocity which decays to pressure equilibrium during diffusion. At early times, the diffusive process generates pressure and velocity waves which propagate outward from the interface and are required to maintain momentum conservation. The energy in the outgoing waves dissipates as heat in viscous regions, and it is hypothesized that these diffusion driven waves may sustain fluctuations in less viscid finite domains after reflections from the boundaries. Finally, these fluid dynamic phenomena are similar in gases or plasmas and occur in flow transients with a moderate Knudsen number. The analysis and simulation results show how the kinetic flux, represented in the fluid transport closure, directly modifies the mass averaged flow described with the Euler equations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Grain detachment and transport clogging during mineral dissolution in carbonate rocks with permeable grain boundaries

In this paper, we explore the effect of permeable grain boundaries on carbonate rock dissolution in order to improve our understanding of grain detachment and migration during reactive flow. To do so we investigated the effects of grain size and enhanced reactivity along grain boundaries on global dissolution kinetics. Variations of permeability and porosity were calculated, and exponential relationships were observed in fractured rocks. Our model employed a reactive transport framework based on the Darcy-Brinkman equation to simulate calcite dissolution in carbonate rocks composed of microporous grains and, included fluid transport along grain boundaries. The model includes fluid flow, solute transport by advection–diffusion, heterogeneous reaction between fluid and minerals and grain detachment with subsequent grain transport in macropores. The migration of solid particles due to dissolution was based on cluster analysis and local movement, and the results show that grain detachment can lead to significant decreases in permeability due to the clogging of transport pathways. Microporous media with smaller grain sizes (fine grains in this study) showed a higher average reaction rate than those with coarser grains. In addition, as the overall rates of geochemical processes are commonly affected by the presence of texture heterogeneities such as fractures, a single fracture (macropore) introduced into a microporous matrix composed of permeable grains and grain boundaries was modelled as a large channel connecting the inlet and outlet of the simulation domain. It was found that macropore clogging by grain detachment temporary decreased permeability, lowering the long-term global reaction rates. Lastly, we observed that increases in flow rate can reduce detachment and fracture clogging by reducing local dissolution along grain boundaries.

58 GEOSCIENCES↗

The Techniques of Surface Alignment of Liquid Crystals

Alignment of liquid crystal (LC) molecules is an important topic of physics of anisotropic fluids. Here, the boundary conditions and the surface properties of the material in contact with an LC dictate the preferred orientation of the molecules at the interface.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Uncoupling Electrokinetic Flow Solutions

The continuum-scale electrokinetic porous-media flow and excess charge redistribution equations are uncoupled using eigenvalue decomposition. The uncoupling results in a pair of independent diffusion equations for “intermediate” potentials subject to modified material properties and boundary conditions. The fluid pressure and electrostatic potential are then found by recombining the solutions to the two intermediate uncoupled problems in a matrix-vector multiplication. Expressions for the material properties or source terms in the intermediate uncoupled problem may require extended precision or careful rewriting to avoid numerical cancellation, but the solutions themselves can typically be computed in double precision. The approach works with analytical or gridded numerical solutions and is illustrated through two examples. The solution for flow to a pumping well is manipulated to predict streaming potential and electroosmosis, and a periodic one-dimensional analytical solution is derived and used to predict electroosmosis and streaming potential in a laboratory flow cell subjected to low frequency alternating current and pressure excitation. The examples illustrate the utility of the eigenvalue decoupling approach, repurposing existing analytical solutions or numerical models and leveraging solutions that are simpler to derive for coupled physics.

58 GEOSCIENCES↗

Micromechanical processes in consolidated granular salt

Here, granular salt is likely to be used as backfill material and a seal system component within geologic salt formations serving as a repository for long-term isolation of nuclear waste. Pressure from closure of the surrounding salt formation will promote consolidation of granular salt, eventually resulting in properties comparable to native salt. Understanding dependence of consolidation processes on stress state, moisture availability, temperature, and time is important for demonstrating sealing functions and long-term repository performance. This study characterizes laboratory-consolidated granular salt by means of microstructural observations. Granular salt material from mining operations was obtained from the bedded Salado Formation hosting the Waste Isolation Pilot Plant and the Avery Island salt dome. Laboratory test conditions included hydrostatic consolidation of jacketed granular salt with varying conditions of confining isochoric stress to 38 MPa, temperature to 250 °C, moisture additions of 1% by weight, time duration, and vented and non-vented states. Resultant porosities ranged between 1% and 22%. Optical and scanning electron microscopic techniques were used to ascertain consolidation mechanisms. From these investigations, samples with 1% added moisture or unvented during consolidation, exhibit clear pressure solution processes with tightly cohered grain boundaries and occluded fluid pores. Samples with only natural moisture content consolidated by a combination of brittle, cataclastic, and crystal plastic deformation. Recrystallization at 250 °C irrespective of moisture conditions was also observed. The range and variability of conditions applied in this study, combined with the techniques used to display microstructural features, are unique, and provide insight into an important area of governing deformation mechanism(s) occurring within salt repository applications.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Core-scale numerical simulation and comparison of breakdown of shale and resulting fractures using sc-CO 2 and water as injectants

Supercritical carbon dioxide (sc-CO 2 ) is an alternative to water for stimulation of low permeability systems such as shale gas and geothermal resources. Previously core-scale experimental studies have compared the behavior of CO 2 to water injection for sample breakdown. Due to differences in experimental setup and core sample preparation, inconsistent or even apparently contradictory conclusions have resulted. To reconcile this contradiction, a phase-field numerical model is applied to understand hydraulic fracturing experiments using Green River shale found in the literature. The finite element numerical model incorporates a rate-dependent phase-field fracture model developed separately to describe fracture initiation and growth. We investigate the impact of various material and fluid properties on the resulting fractures. Most importantly, we study the effect of fluid properties and boundary conditions on the breakdown pressure, including the direction of the resulting fracture plane. Model results predict that (1) sc-CO 2 injection in the laboratory may result in greater breakdown pressure than that of water under no-flow boundary conditions because lower viscosity sc-CO 2 may result in pressure build up at the core boundary that opposes fracture initiation and (2) lower viscosity sc-CO 2 also produces fast-propagating fractures that are less influenced by the bedding plane on their resulting fracture topology. Here our model offers a straightforward explanation and reconciliation of existing experimental observations, as well as a means to extrapolate to new conditions. Exploration of field-scale conditions suggests less pronounced or no elevation in breakdown pressure when sc-CO 2 is injected because the pressure build up effect at the system boundary is significantly less or absent at field length scales.

42 ENGINEERING↗

Inertial impedance of coalescence during collision of liquid drops

The fluid dynamics of the collision and coalescence of liquid drops has intrigued scientists and engineers for more than a century owing to its ubiquitousness in nature, e.g. raindrop coalescence, and industrial applications, e.g. breaking of emulsions in the oil and gas industry. The complexity of the underlying dynamics, which includes occurrence of hydrodynamic singularities, has required study of the problem at different scales – macroscopic, mesoscopic and molecular – using stochastic and deterministic methods. In this work, a multi-scale, deterministic method is adopted to simulate the approach, collision, and eventual coalescence of two drops where the drops as well as the ambient fluid are incompressible, Newtonian fluids. The free boundary problem governing the dynamics consists of the Navier–Stokes system and associated initial and boundary conditions that have been augmented to account for the effects of disjoining pressure as the separation between the drops becomes of the order of a few hundred nanometres. This free boundary problem is solved by a Galerkin finite element-based algorithm. The interplay of inertial, viscous, capillary and van der Waals forces on the coalescence dynamics is investigated. It is shown that, in certain situations, because of inertia two drops that are driven together can first bounce before ultimately coalescing. This bounce delays coalescence and can result in the computed value of the film drainage time departing significantly from that predicted from existing scaling theories.

Mechanics↗

Unsteady- and Steady-State Relative Permeability Study with X-ray and Acoustic Monitoring for CO 2 Storage in Deep Saline Aquifers

In this study, we link the multiphase flow measurements with controls of sedimentary structures (e.g., heterogeneity and anisotropy) on relative permeability to variations in ultrasonic velocities for two deep saline aquifer formations (Entrada and Bluff Sandstones) in the San Juan Basin of the Southwestern USA. The rock specimens were extracted from outcrop sites near Durango, CO, USA. They have distinct differences in grain size, cementation composition, and individual chemical amounts, despite both formations being eolian sandstones. We performed a series of unsteady- and steady-state CO 2 -brine relative permeability experiments under capillary-controlled displacement rates. Unsteady-state experiments were conducted at 71 °C and 9.65 MPa; steady-state experiments were conducted at 85 °C and 22.8 MPa and 89 °C and 24.1 MPa for the Bluff and Entrada Sandstones, respectively. During the unsteady experiments, X-ray computed tomography was used to visualize multiphase flow in porous media and quantify saturations during brine drainage under various flow rates. Scan images and saturation profiles indicate that the CO 2 distribution in the pore volume was strongly impacted by the presence of high-angle cross-laminations, heterogeneous rock structure, and direction of bedding orientation. Those factors contribute to dramatic and quick initial breakthroughs and affect the overall saturation dynamics. Steady-state relative permeability tests were conducted at net flow rates of 1 mL/min for both brine drainage and imbibition. During the experimental steps, the CO 2 fractional flow was increased and decreased for both drainage and imbibition scenarios to mimic the front when CO 2 contacts brine and behind the front when brine enters space previously occupied by CO 2 . It was found that compressional velocity decreased, while shear waves slightly increased as brine saturation decreased. The hysteresis effects for the relative permeability and acoustic velocities were distinct. Furthermore, the CO 2 /brine front stability is quantified by applying a mobility ratio approach to spot saturations at which the boundary line between fluids becomes uneven. The results presented in this work can potentially boost the quality and precision of forecasts for the CO 2 storage projects in which the vertical and horizontal core-scale heterogeneity and anisotropy impact the plume migration within host reservoirs.

carbon dioxide (CO2)↗

A platform for studying the Rayleigh–Taylor and Richtmyer–Meshkov instabilities in a planar geometry at high energy density at the National Ignition Facility

A new experimental platform has been developed at the National Ignition Facility (NIF) for studying the Rayleigh–Taylor (RT) and Richtmyer–Meshkov (RM) instabilities in a planar geometry at high-energy-densities. The platform uses 60 beams of the NIF laser to drive an initially solid shock tube containing a pre-machined interface between dense and light materials. The strong shock turns the initially solid target into a plasma and the material boundary into a fluid interface with the imprinted initial condition. The interface evolves by action of the RT and RM instabilities, and the growth is imaged with backlit x-ray radiography. We present our first data involving sinusoidal interface perturbations driven from the heavy side to the light side. Late-time radiographic images show the initial conditions reaching the deeply nonlinear regime, and an evolution of fine structure consistent with a transition to turbulence. Lastly, we show preliminary comparisons with post-shot numerical simulations and discuss the implications for future campaigns.

36 MATERIALS SCIENCE↗

Statistical inference of anomalous thermal transport with uncertainty quantification for interpretive 2D SOL models

The critical task of inferring anomalous cross-field transport coefficients is addressed in simulations of boundary plasmas with fluid models. A workflow for parameter inference in the UEDGE fluid code is developed using Bayesian optimization with parallelized sampling and integrated uncertainty quantification. In this workflow, transport coefficients are inferred by maximizing their posterior probability distribution, which is generally multidimensional and non-Gaussian. Uncertainty quantification is integrated throughout the optimization within the Bayesian framework that combines diagnostic uncertainties and model limitations. As a concrete example, we infer the anomalous electron thermal diffusivity $\chi_\perp$ from an interpretive 2D model describing electron heat transport in the conduction-limited region with radiative power loss. The workflow is first benchmarked against synthetic data and then tested on H-, L-, and I-mode discharges to match their midplane temperature and divertor heat flux profiles. We demonstrate that the workflow efficiently infers diffusivity and its associated uncertainty, generating 2D profiles that match 1D measurements. Future efforts will focus on incorporating more complicated fluid models and analyzing transport coefficients inferred from a large database of experimental results.

Bayesian optimization↗

Membrane perturbing properties of toxin mycolactone from Mycobacterium ulcerans

Mycolactone is the exotoxin produced by Mycobacterium ulcerans and is the virulence factor behind the neglected tropical disease Buruli ulcer. The toxin has a broad spectrum of biological effects within the host organism, stemming from its interaction with at least two molecular targets and the inhibition of protein uptake into the endoplasmic reticulum. Although it has been shown that the toxin can passively permeate into host cells, it is clearly lipophilic. Association with lipid carriers would have substantial implications for the toxin’s distribution within a host organism, delivery to cellular targets, diagnostic susceptibility, and mechanisms of pathogenicity. Yet the toxin’s interactions with, and distribution in, lipids are unknown. Herein we have used coarse-grained molecular dynamics simulations, guided by all-atom simulations, to study the interaction of mycolactone with pure and mixed lipid membranes. Using established techniques, we calculated the toxin’s preferential localization, membrane translocation, and impact on membrane physical and dynamical properties. The computed water-octanol partition coefficient indicates that mycolactone prefers to be in an organic phase rather than in an aqueous environment. Our results show that in a solvated membrane environment the exotoxin mainly localizes in the water-membrane interface, with a preference for the glycerol moiety of lipids, consistent with the reported studies that found it in lipid extracts of the cell. The calculated association constant to the model membrane is similar to the reported association constant for Wiskott-Aldrich syndrome protein. Mycolactone is shown to modify the physical properties of membranes, lowering the transition temperature, compressibility modulus, and critical line tension at which pores can be stabilized. It also shows a tendency to behave as a linactant, a molecule that localizes at the boundary between different fluid lipid domains in membranes and promotes inter-mixing of domains. This property has implications for the toxin’s cellular access, T-cell immunosuppression, and therapeutic potential.

59 BASIC BIOLOGICAL SCIENCES↗

Truchas-Flow

The truchas flow algorithm is designed for simulating the behavior of incompressible (but not necessarily constant density) fluids on unstructured meshes while allowing for solid and void phases to serve as moving boundaries. The interface between fluids, solids and void is tracked via a geometric volume of fluid approach. This allows for a single fluid formulation of the governing equations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Development and Validation of a Conjugate Heat Transfer Model for the Two-Phase CFD Code NEK-2P

A project is underway to develop, verify and validate an advanced two-phase flow modeling capability for the highly-scalable, high-performance CFD code NEK5000. The goal of the project is to develop a new two-phase version of the NEK5000 code, named NEK-2P, to simulate the two-phase flow and heat transfer phenomena that occur in a Boiling Water Reactor (BWR) fuel bundle under various operating conditions. The NEK-2P two-phase flow models follow the approach used for the Extended Boiling Framework (EBF) [2-3] previously developed at Argonne, but include more fundamental physical models of boiling phenomena and advanced numerical algorithms for improved computational accuracy, robustness, and computational speed. The development of the NEK-2P two-phase solver and the implementation of the Extended Boiling Framework two-phase models were initially supported by Argonne National Laboratory (Argonne) through a Laboratory Directed Research and Development (LDRD) project during FY2014-2016. The development and validation of the two-phase models through analyses of selected two-phase boiling flow experiments was supported by the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program in FY2017-2019. This report focuses on the FY2019 development and validation of the Conjugate Heat Transfer (CHT) model for the NEK-2P Two-Phase, Computational Fluid Dynamics (CFD) code. The NEK-2P CHT model calculates the coupled behavior of the fluid and solid domains. In the fluid domain NEK-2P calculates the vapor and liquid phase temperatures, velocities and mass fractions. In the solid domain only the temperatures are calculated. The fluid and solid domains are coupled with a heat flux boundary condition at the fluid-solid interface. The heat flux and the wall temperatures at the fluid-solid interface are updated using the NEK-2P wall heat-flux partitioning model. A wall heat flux boundary condition is also applied to the exterior surface of the solid domain. The CHT model validation was illustrated through the analysis of three of the Becker Critical Heat Flux (CHF) tests. Reasonably good agreement with measured data was obtained in predicting the CHF location and post CHF wall temperature behavior illustrating the ability of the NEK-2P CHT model to simulate the CHF phenomena for a wide range of thermal-hydraulic conditions. Apart from the CHT model development and validation, initial simulations were performed for the Virginia Tech. (VT) 3x3 bare rod bundle experiments including both cold and boiling flow simulations.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Investigating the Interaction Between Circulating Tumor Cells and Local Hydrodynamics via Experiment and Simulations

Introduction: The biological and mechanical properties of circulating tumor cells (CTCs) in combination with the hemodynamics affect the preference of metastatic sites in the vasculature. Despite the extensive literature on the effects of biological properties on cell adhesion, the effects of hydrodynamic forces on primary attachment remains an active area of research. Here, using simulations in conjunction with experimentation, we provide new insight into the interplay of CTCs dynamics and local hydrodynamics. Methods: A flow experiment of CTC attachment was performed within a bioprinted, double branching endothelialized vessel. Simulations of fluid flow and CTC transport in the reconstructed and idealized bifurcated vessel were respectively performed by HARVEY, our in-house massively parallel computational fluid dynamics solver. HARVEY is based on the lattice Boltzmann and finite element methods to model the fluid and cells dynamics. The immersed boundary method is employed for resolving the fluid–structure interaction. Results: CTC attachment was quantified experimentally at all regions of the complex vessel. The results demonstrate a clear preference for CTCs to attach at the branch points. To elucidate the effect of the vessel topology on the location of attachment, a fluid-only simulation was performed assessing the differences in the hydrodynamics along the vessel. CTC transport in idealized bifurcated vessels was subsequently studied to examine the effects of cell deformability on the local hydrodynamics patterns and, thus, the preference of attachment sites. Conclusions: The current work provides evidence on the correlation of the hydrodynamics forces arising from the vessel topology and CTC properties on the attachment regions.

60 APPLIED LIFE SCIENCES↗