Bulletin of the American Physical Society
72nd Annual Meeting of the APS Division of Fluid Dynamics
Volume 64, Number 13
Saturday–Tuesday, November 23–26, 2019; Seattle, Washington
Session L29: Biological Fluid Dynamics : Multiscale Biofluids |
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Chair: Gwynn Elfring, UBC Room: 611 |
Monday, November 25, 2019 1:45PM - 1:58PM |
L29.00001: A CFD-based design of a microfluidic platform for separating blood cells Anoop Kanjirakat, Zhang Han, Reza Sadr, Arum Han Point-of-care (PoC) diagnostic systems utilizing microfluidic platforms are becoming popular in the detection of biomarkers in blood samples. In this work, we aim to develop a passive plasma separator that can be effectively integrated into a blood diagnosis system for detecting cardiovascular biomarkers. A single-step process of creating a cell-free region in the flow without the plasma being actively extracted from the whole blood is envisaged. Sensors are proposed to be placed in the cell-free zones for biomarker detection. A two-phase numerical study to investigate the various geometrical factors affecting the development of a cell-free zone in the backward-facing step of an expansion chamber is made. The cellular particle interactions in the blood are modeled using a discrete element method (DEM). The sizes of the cell-free zones in the microfluidic system are studied for 18 different geometric configurations. Cell-free radius is estimated with an accuracy of 10 micrometers. An expansion chamber with a larger aspect ratio together with a low Reynold number flow entering it is observed to create a larger cell-free zone. The numerical observations are initially validated with the flow of fluorescent beads and later using diluted blood samples. [Preview Abstract] |
Monday, November 25, 2019 1:58PM - 2:11PM |
L29.00002: A multiphysics computational model for design and optimization of drug transport in an endovascular Chemofilter device Nazanin Maani, Tyler C. Diorio, Stephen W. Hetts, Vitaliy L. Rayz The effectiveness of Intra-arterial chemotherapy (IAC) is limited by the majority of drugs, e.g. Doxorubicin (Dox), that pass into systemic circulation and cause cardiac toxicity. These excessive drugs can be captured by the Chemofilter (CF) -- a 3D-printable, catheter based device deployed in a vein downstream of the liver during IAC. The CF chemically adsorbs Dox via ion-exchange with a surface-coated resin. In this study, the CF hemodynamic performance and drug transport were evaluated with multiphysics computational modeling. Device design was optimized using a sensitivity analysis of flow and geometry parameters. The electrochemical binding was modeled based on concentrated solution theory, where diffusion and ion migration were incorporated into an effective diffusivity term. The Navier-Stokes and Advection-Diffusion-Reaction equations were coupled in ANSYS Fluent. The optimized CF consists of an array of hexagonal channels that are twisted, perforated, and aligned with the flow direction to enhance mixing and drug binding. The optimized CF results in a 66.8{\%} drug reduction and pressure drop of 3mm Hg, with model validation by in-vivo porcine studies. These results demonstrate the utility of the CF in improving IAC performance while preventing flow stagnation regions. [Preview Abstract] |
Monday, November 25, 2019 2:11PM - 2:24PM |
L29.00003: From ab-initio Mesoscale Modelling of Red Blood Cells Towards Macroscale Simulations in Biomedical Devices Fabio Guglietta, Luca Biferale, Giacomo Falcucci, Mauro Sbragaglia, Marek Behr, Giannis Koutsou Ventricular assist devices (VADs) are mechanical pumps which are designed to assist the blood circulation in people with heart problems. One important challenge is to minimise the blood damage (haemolysis) in the pump; to this aim, computational fluid dynamics has gained an increasing deal of attention in the recent years. The most recent computational fluid dynamics approaches use tensor-based (TB) models, wherein the red blood cells (RBCs) are modelled as deforming suspensions evolving in the flow, and their deformation is used to measure the shear stress and correlate it to the haemolysis. The aim of this work is to improve the TB model through ab-initio simulations of the single RBC. Specifically, we have used a hybrid Immersed Boundary-Lattice Boltzmann Method (IB-LBM) code to perform numerical simulations of a single RBC suspended in a simple shear flow. After a validation of the IB-LBM model, the ab-initio simulations will be interfaced with TB models and quantitative comparisons of the deformation history coming from both models will be provided. The expected outcome is a quantitative protocol to adapt the TB model parameters to the flow and structure properties. [Preview Abstract] |
Monday, November 25, 2019 2:24PM - 2:37PM |
L29.00004: Computational modeling of bacterial dynamics under shear flow Kartik Jain, Christoph Lohrmann, Christian Holm Bacteria can propel, proliferate and accumulate in a number of media and their dynamics are affected by shear flow. In addition to self-propulsion, bacteria can stick to each other and to surfaces where they can create fast growing colonies, called biofilm. Studies have shown that bacteria more commonly accumulate at surfaces and around obstacles. In the present work we modeled dynamics of E.Coli in a water like fluid. In the model the bacteria are represented by molecular dynamics (MD) particles while the fluid is represented by a lattice Boltzmann method (LBM). The MD particles are coupled to the LB fluid using a frictional point coupling that ensures momentum conservation of the total system. We present collective transient dynamics of up to 4000 bacteria in porous configurations. Our results show that the bacteria tend to a state of momentary stasis in regions where the underlying fluid recirculates, and thus result in a sticking behavior near the obstacles of the porous media. Our findings indicate that such a behavior is manifested mainly due to hydrodynamics interactions between a bacterium and the surfaces. Our model of bacterial replication agrees well with experimental data and ongoing work includes coupling of time scales in bacterial life cycle to model biofilms. [Preview Abstract] |
Monday, November 25, 2019 2:37PM - 2:50PM |
L29.00005: Efflux Pumping Mechanism of AcrB in Multidrug Resistance Bacteria Quyen Dinh, Jin Liu, Prashanta Dutta The AcrB is a multidrug pump in gram-negative bacteria responsible for ejecting antibiotics and other metabolic waste for its survival. Thus, understanding the expelling mechanisms of AcrB is essential in designing successful drugs. Though crystal structure of AcrB can be captured by the X-ray diffraction, the molecular details of AcrB-drug interaction are difficult to be identified by experiment. We have developed a hybrid coarse-grained molecular dynamics (MD) model to capture conformational changes of AcrB in presence of drug candidates at the distal binding pocket to understand the efflux mechanism. Binding energy of drugs with AcrB and potential of mean force (PMF) on drugs along the expelling pathway are also calculated. Our MD simulations show that AcrB monomer changes from binding state to extrusion state in the presence of drug or other substrate, if transmembrane residues Asp407 and/or 408 are being protonated by an antiport mechanism. Moreover, computed binding energy and PMF reveals that inhibitor-like drugs bind with AcrB much stronger than metabolic waste or conventional antibiotics. Our study suggests that inhibitor-like multifunctional drugs could effectively block AcrB pumping. [Preview Abstract] |
Monday, November 25, 2019 2:50PM - 3:03PM |
L29.00006: ABSTRACT WITHDRAWN |
Monday, November 25, 2019 3:03PM - 3:16PM |
L29.00007: Multiscale modeling of thrombus formation and its application in simulating the development of thrombus in retinal microaneurysms He Li, Xiaoning Zheng, Alireza Yazdani, Sampani Konstantina, Jennifer Sun, George Karniadakis I will present methods for atomistc-continuum coupling that enable multi-fidelity modeling of the multiscale processes taking place in thrombus formation and in the early stages. We use dissipative particle dynamics, force coupling methods and phase field methods to bridge different time and spatial scales involved in the thrombus formation process. Specifically, we simulate the aggregation of platelets by coupling a spectral/hp element method with a force coupling method. Once platelets aggregate, we convert the platelet distribution into a three-dimensional continuum field to estimate the clot volume fraction, which serves as an input for the phase-field simulation. Then, we use the phase-field method to simulate the interaction between the formed thrombus and flowing blood. At last, I will show some preliminary results from implementation of this framework to model the formation of thrombus in retinal microaneurysm, a sign of initial stage diabetic retinopathy. [Preview Abstract] |
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