Coupled Flow-Biochemistry Simulations of Dynamic Systems of Blood Cells

Open Access
Author:
Gaskin, Byron Jerrod
Graduate Program:
Mechanical Engineering
Degree:
Master of Science
Document Type:
Master Thesis
Date of Defense:
None
Committee Members:
  • Robert Francis Kunz, Thesis Advisor
  • Brent Craven, Thesis Advisor
Keywords:
  • computational fluid dynamics
  • CFD
  • stokes flow
  • blood cells
  • 6DOF
  • six degrees-of-freedom
  • biochemistry
Abstract:
With the aim of improved modeling of biological cell flow simulations, a computational tool has been developed to model a heterogeneous system comprised of an arbitrary number of bodies of arbitrary geometry interacting in highly viscous flows. Accordingly, this model couples computational fluid dynamics (CFD), six degree-of-freedom (6DOF) motion, and surface biochemistry. Adaptive mesh refinement is used to ensure adequate resolution of flow features when multiple surfaces are in close proximity. The particular contributions of this thesis include: 1) stability analysis of the coupled 6DOF-hydrodynamics system, leading to an efficient adaptive timestep specification, 2) introduction of the immersed boundary method (IBM), wherein arbitrary cell shapes are meshed internally, to enable exact inertial property evaluations, and 3) generalization to an n-body system including a novel cyclic method for reintroducing cells on periodic boundaries to enable statistical stationarity. These and other improvements presented in this thesis have led to a tool with improved modeling accuracy and computer run times that are orders of magnitude faster than its predecessor. The capabilities of this tool are demonstrated by presenting several three-dimensional cell system simulations. The presented cell system simulations are found to be in agreement with data found in the literature.