Browsing by Author "Owkes, Mark"

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Biofilm.jl: A fast solver for one-dimensional biofilm chemistry and ecology
(Elsevier BV, 2023-12) Owkes, Mark; Coblentz, Kai; Eriksson, Austen; Kammerzell, Takumi; Stewart, Philip S.
Biofilms are communities of microorganisms that grow on virtually all surfaces with sufficient nutrients including aquatic and industrial water systems and medical devices. Biofilms are complex, structured communities where the interplay of growth, metabolism, and competition between species interact with physical processes of diffusion, convection, attachment, and detachment. This work describes a model of a one-dimensional biofilm in a stirred tank reactor that incorporates these complexities. The model is implemented in the modern Julia programming language providing an efficient tool for studying a large variety of biofilms and the intricate communities the microorganisms create. Details of the new software, known as Biofilm.jl, including the mathematical model and organization and execution of the code, are provided. Examples of biofilms modeled using Biofilm.jl are presented such as a single heterotroph, sulfide-oxidizing bacteria (SOB) and sulfate-reducing bacteria (SRB), and a phototroph. Postprocessing tools are described that allow a Biofilm.jl user to make plots and extract specific values from the solution and explore the simulated biofilm results.
Efficient extraction of atomization processes from high-fidelity simulations
(Elsevier BV, 2023-02) Christensen, Brendan; Owkes, Mark
Understanding the process of primary and secondary atomization in liquid jets is crucial in describing spray distribution and droplet geometry for industrial applications and is essential in the development of physics-based low-fidelity atomization models that can quickly predict these sprays. Significant advances in numerical modeling and computational resources allow research groups to conduct detailed numerical simulations and accurately predict the physics of atomization. These simulations can produce hundreds of terabytes of data. The substantial size of these data sets limits researchers’ ability to analyze them. Consequently, the process of a coherent liquid core breaking into droplets has not been analyzed in simulation results even though a complete description of the jet dynamics exists. The present work applies a droplet physics extraction technique to high-fidelity simulations to track breakup events as they occur and extract data associated with the local flow. The data on the atomization process are stored in a Neo4j graphical database providing an easily accessible format. Results provide a robust, quantitative description of the process of atomization and the details on the local flow field will be useful in the development of low-fidelity atomization models.
A fast, decomposed pressure correction method for an intrusive stochastic multiphase flow solver
(2021-05) Turnquist, Brian; Owkes, Mark
Solution of the pressure Poisson equation is often the most expensive aspect of solving the incompressible form of Navier–Stokes. For a single phase deterministic model the pressure calculation is costly. Expanded to an intrusive stochastic multiphase framework, the simulation expense grows dramatically due to coupling between the stochastic pressure field and stochastic density. To address this issue in a deterministic framework, Dodd and Ferrante (“A fast pressure-correction method for incompressible two-fluid flows” Journal of Computational Physics, 273, 416–434, 2014) discuss a decomposed pressure correction method which utilizes an estimated pressure field and constant density to modify the standard pressure correction method. The resulting method is useful for improving computational cost for one-fluid formulations of multiphase flow calculations. In this paper, we extend the decomposed pressure correction method to intrusive uncertainty quantification of multiphase flows. The work improves upon the original formulation by modifying the estimated pressure field. The new method is assessed in terms of accuracy and reduction in computational cost with oscillating droplet, damped surface wave, and atomizing jet test cases where we find convergence of results with the proposed method to those of a traditional pressure correction method and analytic solutions, where appropriate.
Heat conduction simulation of chondrocyte-embedded agarose gels suggests negligible impact of viscoelastic dissipation on temperature change
(Elsevier BV, 2024-09) Myers, Erik; Piazza, Molly; Owkes, Mark; June, Ronald K.
Agarose is commonly used for 3D cell culture and to mimic the stiffness of the pericellular matrix of articular chondrocytes. Although it is known that both temperature and mechanical stimulation affect the metabolism of chondrocytes, little is known about the thermal properties of agarose hydrogels. Thermal properties of agarose are needed to analyze potential heat production by chondrocytes induced by various experimental stimuli (carbon source, cyclical compression, etc). Utilizing ASTM C177, a custom-built thermal conductivity measuring device was constructed and used to calculate the thermal conductivity of 4.5 % low gelling temperature agarose hydrogels. Additionally, Differential Scanning Calorimetry was used to calculate the specific heat capacity of the agarose hydrogels. Testing of chondrocyte-embedded agarose hydrogels commonly occurs in Phosphate-Buffered Saline (PBS), and thermal analysis requires the free convection coefficient of PBS. This was calculated using a 2D heat conduction simulation within MATLAB in tandem with experimental data collected for known boundary and initial conditions. The specific heat capacity and thermal conductivity of 4.5 % agarose hydrogels was calculated to be 2.85 J/g°C and 0.121 W/mK, respectively. The free convection coefficient of PBS was calculated to be 1000.1 W/m2K. The values of specific heat capacity and thermal conductivity for agarose are similar to the reported values for articular cartilage, which are 3.20 J/g°C and 0.21 W/mK (Moghadam, et al. 2014). These data show that cyclical loading of hydrogel samples with these thermal properties will result in negligible temperature increases. This suggests that in addition to 4.5 % agarose hydrogels mimicking the physiological stiffness of the cartilage PCM, they can also mimic the thermal properties of articular cartilage for in vitro studies.
High-fidelity simulations of a rotary bell atomizer with electrohydrodynamic effects
(Elsevier BV, 2023-11) Krisshna, Venkata; Liu, Wanjiao; Owkes, Mark
Electrostatic rotary bell atomizers are extensively used as paint applicators in the automobile industry. Paint undergoes atomization after exiting the edge of a high-speed rotating bell. In most setups, the paint is electrically charged and a background electric field is applied between the nozzle and the target surface to increase the transfer efficiency (TE). The atomization process directly determines the droplet size and droplet charge distributions which subsequently control TE and surface finish quality. Optimal spray parameters used in industry are often obtained from expensive trial-and-error methods. In this work, three-dimensional near-bell atomization is computationally simulated using a high-fidelity volume-of-fluid transport scheme that includes electrohydrodynamic (EHD) effects. We find that electrifying the setup results in the production of smaller droplets. Additionally, the electric field has a minor effect on primary atomization but a negligible effect on the size and stability of atomized droplets after secondary breakup. This cost-effective method of simulating EHD-assisted atomization allows for the understanding of the effect of the electric field and the extraction of droplet charge characteristics which is otherwise challenging to obtain experimentally.
Investigating atomization characteristics in an electrostatic rotary bell atomizer
(Elsevier BV, 2024-05) Krisshna, Venkata; Owkes, Mark
Electrostatic rotary bell atomizers are commonly used in several engineering applications, including the automobile industry. A high-speed rotating nozzle operating in a strong background electric field atomizes paint into charged droplets that range from a few micrometers to tens of micrometers in diameter. The atomization process directly determines the droplet size and droplet charge distributions which subsequently control the transfer efficiency and the surface finish quality. We have previously developed a tool to perform high fidelity simulations of near-bell atomization with electrohydrodynamic effects. In this work, we perform simulations employed with a droplet ancestry extraction tool to analyze previously inaccessible information and understand the physical processes driving atomization. We find that the electric field accelerates breakup processes and enhances secondary atomization. The total number of droplets, the ratio of secondary to primary droplets, and the ratio of coalescence to breakup activity are all much higher when operating in an electric field. We analyze the droplet velocity, local Weber number and charge density statistics to understand the complex physics in electrically assisted breakup. The results of the study have helped us gain insights into the physics of atomization in electrostatic rotary sprays.
A mass and momentum conserving unsplit semi-Lagrangian framework for simulating multiphase flows
(2017-03) Owkes, Mark; Desjardins, Olivier
In this work, we present a computational methodology for convection and advection that handles discontinuities with second order accuracy and maintains conservation to machine precision. This method can transport a variety of discontinuous quantities and is used in the context of an incompressible gasâ€“liquid flow to transport the phase interface, momentum, and scalars. The proposed method provides a modification to the three-dimensional, unsplit, second-order semi-Lagrangian flux method of Owkes & Desjardins (JCP, 2014). The modification adds a refined grid that provides consistent fluxes of mass and momentum defined on a staggered grid and discrete conservation of mass and momentum, even for flows with large density ratios. Additionally, the refined grid doubles the resolution of the interface without significantly increasing the computational cost over previous non-conservative schemes. This is possible due to a novel partitioning of the semi-Lagrangian fluxes into a small number of simplices. The proposed scheme is tested using canonical verification tests, rising bubbles, and an atomizing liquid jet.
MultiUQ: A software package for uncertainty quantification of multiphase flows
(2021-11) Turnquist, Brian; Owkes, Mark
multiUQ is a novel tool that simulates gas-liquid multiphase flows and quantifies uncertainty in results due to variability about fluid properties and initial/boundary conditions. The benefit over a typical deterministic solver is that inexact information, such as variability in fluid properties or flow rates, can be included to determine the affect on simulation solutions. It is common to deploy non-intrusive methods which utilize many solutions from a deterministic solver to generate a distribution of possible results. Contrarily, multiUQ uses an intrusive uncertainty quantification method wherein variables of interest are functions of space, time, and additional uncertainty dimensions. The intrusive solver is run once, giving a distribution of solutions as an output, as well as desired statistics. We use polynomial chaos to create the stochastic variables, which represent a distribution of values at each grid point. The stochastic variables are substituted into the incompressible Navier-Stokes equations, which govern the stochastic fluid dynamics. A stochastic level set is used to capture the distribution of interfaces that are present in an uncertain multiphase flow. multiUQ is written in Fortran and uses a message passing interface (MPI) for parallel operation. Given the many applications of multiphase flows, including open flows, hydraulics, fuel injection systems, and atomizing jets, there is a massive potential benefit to calculating uncertainty information about these flows in a cost-effective manner.
Simulation of catalase-dependent tolerance of microbial biofilm to hydrogen peroxide with a biofilm computer model
(Springer Science and Business Media LLC, 2023-08) Stewart, Philip S.; Owkes, Mark
Hydrogen peroxide (HP) is a common disinfectant and antiseptic. When applied to a biofilm, it may be expected that the top layer of the biofilm would be killed by HP, the HP would penetrate further, and eventually eradicate the entire biofilm. However, using the Biofilm.jl computer model, we demonstrate a mechanism by which the biofilm can persist, and even become thicker, in the indefinite treatment with an HP solution at concentrations that are lethal to planktonic microorganisms. This surprising result is found to be dependent on the neutralization of HP by dead biomass, which provides protection for living biomass deeper within the biofilm. Practically, to control a biofilm, this result leads to the concept of treating with an HP dose exceeding a critical threshold concentration rather than a sustained, lower-concentration treatment.
Three-Dimensional Velocity and Concentration Measurements and Simulations of a Scaled Jack Rabbit II Mock Urban Array
(2020-07) Owkes, Mark; Benson, Michael; Elkins, Christopher; Wilde, Nicholas; Van Poppel, Bret
Magnetic resonance (MR) techniques provide non-invasive, three-dimensional measurements of velocity and concentration fields. Applying MR techniques to measure flows of contaminants through urban arrays provides a wealth of information that is difficult to obtain with large-scale field tests. In this project, a 1:188 scaled model of the phase 1 Jack Rabbit II field test was replicated and studied using a water tunnel with properties chosen to mimic field conditions. Three-dimensional, time-averaged flow data was measured using magnetic resonance velocimetry (MRV) and magnetic resonance concentration (MRC) techniques. The scaled flow was also modeled with large-eddy simulations (LES) to provide a dataset for comparison with the MR based measurements. Despite a complex, three-dimensional flow field, both velocity and concentration show good agreement between the experimental measurements and simulation data. Measurement uncertainty was estimated to be of each of the measured velocity components at each location for MRV and of the measured concentration at each location for MRC.