A Parallel Computational Method for Simulating Two-Phase Gel Dynamics

We develop a parallel computational algorithm for simulating models of gel dynamics where the gel is described by two phases, a networked polymer and a fluid solvent. The models consist of transport equations for the two phases, two coupled momentum equations, and a volumeaveraged incompressibility constraint. Multigrid with Vanka-type box relaxation scheme is used as preconditioner for the Krylov subspace solver (GMRES) to solve the momentum and incompressibility equations. Through numerical experiments of a model problem, the efficiency, robustness and scalability of the algorithm are illustrated

A Study of Different Modeling Choices For Simulating Platelets Within the Immersed Boundary Method

The Immersed Boundary (IB) method is a widely-used numerical methodology for the simulation of fluid-structure interaction problems. The IB method utilizes an Eulerian discretization for the fluid equations of motion while maintaining a Lagrangian representation of structural objects. Operators are defined for transmitting information (forces and velocities) between these two representations. Most IB simulations represent their structures with piecewise-linear approximations and utilize Hookean spring models to approximate structural forces. Our specific motivation is the modeling of platelets in hemodynamic flows. In this paper, we study two alternative representations - radial basis functions (RBFs) and Fourier-based (trigonometric polynomials and spherical harmonics) representations - for the modeling of platelets in two and three dimensions within the IB framework, and compare our results with the traditional piecewise-linear approximation methodology. For different representative shapes, we examine the geometric modeling errors (position and normal vectors), force computation errors, and computational cost and provide an engineering trade-off strategy for when and why one might select to employ these different representations.Comment: 33 pages, 17 figures, Accepted (in press) by APNU

An Efficient and Robust Method for Simulating Two-Phase Gel Dynamics

We develop a computational method for simulating models of gel dynamics where the gel is described by two phases: a networked polymer and a fluid solvent. The models consist of transport equations for the two phases, two coupled momentum equations, and a volume-averaged incompressibility constraint, which we discretize with finite differences/volumes. The momentum and incompressibility equations present the greatest numerical challenges since (i) they involve partial derivatives with variable coefficients that can vary quite significantly throughout the domain (when the phases separate), and (ii) their approximate solution requires the “inversion” of a large linear system of equations. For solving this system, we propose a box-type multigrid method to be used as a preconditioner for the generalized minimum residual (GMRES) method. Through numerical experiments of a model problem, which exhibits phase separation, we show that the computational cost of the method scales nearly linearly with the number of unknowns and performs consistently well over a wide range of parameters. For solving the transport equation, we use a conservative finite-volume method for which we derive stability bounds

Blood Clot Formation under Flow: The Importance of Factor XI Depends Strongly on Platelet Count

AbstractA previously validated mathematical model of intravascular platelet deposition and tissue factor (TF)-initiated coagulation under flow is extended and used to assess the influence on thrombin production of the activation of factor XI (fXI) by thrombin and of the activation of factor IX (fIX) by fXIa. It is found that the importance of the thrombin-fXIa-fIXa feedback loop to robust thrombin production depends on the concentration of platelets in the blood near the injury. At a near-wall platelet concentration of ∼250,000/μL, typical in vessels in which the shear rate is <200 s−1, thrombin activation of fXI makes a significant difference only at low densities of exposed TF. If the near-wall platelet concentration is significantly higher than this, either because of a higher systemic platelet count or because of the redistribution of platelets toward the vessel walls at high shear rates, then thrombin activation of fXI makes a major difference even for relatively high densities of exposed TF. The model predicts that the effect of a severe fXI deficiency depends on the platelet count, and that fXI becomes more important at high platelet counts

A High-Resolution Finite-Difference Method for Simulating Two-Fluid, Viscoelastic Gel Dynamics

An important class of gels are those composed of a polymer network and fluid solvent. The mechanical and rheological properties of these two-fluid gels can change dramatically in response to temperature, stress, and chemical stimulus. Because of their adaptivity, these gels are important in many biological systems, e.g. gels make up the cytoplasm of cells and the mucus in the respiratory and digestive systems, and they are involved in the formation of blood clots. In this study we consider a mathematical model for gels that treats the network phase as a viscoelastic fluid with spatially and temporally varying material parameters and treats the solvent phase as a viscous Newtonian fluid. The dynamics are governed by a coupled system of time-dependent partial differential equations which consist of transport equations for the two phases, constitutive equations for the viscoelastic stresses, two coupled momentum equations for the velocity fields of the two fluids, and a volume-averaged incompressibility constraint. We present a numerical method based on a staggered grid, second order finite-difference discretization of the momentum equations and a high-resolution unsplit Godunov method for the transport equations. The momentum and incompressibility equations are solved in a coupled manner with the Generalized Minimum Residual (GMRES) method using a multigrid preconditioner based on box-relaxation. We present results on the accuracy and robustness of the method together with an illustration of the interesting behavior of this gel model for the four-roll mill problem