2,383 research outputs found
A parallel interaction potential approach coupled with the immersed boundary method for fully resolved simulations of deformable interfaces and membranes
In this paper we show and discuss the use of a versatile interaction
potential approach coupled with an immersed boundary method to simulate a
variety of flows involving deformable bodies. In particular, we focus on two
kinds of problems, namely (i) deformation of liquid-liquid interfaces and (ii)
flow in the left ventricle of the heart with either a mechanical or a natural
valve. Both examples have in common the two-way interaction of the flow with a
deformable interface or a membrane. The interaction potential approach (de
Tullio & Pascazio, Jou. Comp. Phys., 2016; Tanaka, Wada and Nakamura,
Computational Biomechanics, 2016) with minor modifications can be used to
capture the deformation dynamics in both classes of problems. We show that the
approach can be used to replicate the deformation dynamics of liquid-liquid
interfaces through the use of ad-hoc elastic constants. The results from our
simulations agree very well with previous studies on the deformation of drops
in standard flow configurations such as deforming drop in a shear flow or a
cross flow. We show that the same potential approach can also be used to study
the flow in the left ventricle of the heart. The flow imposed into the
ventricle interacts dynamically with the mitral valve (mechanical or natural)
and the ventricle which are simulated using the same model. Results from these
simulations are compared with ad- hoc in-house experimental measurements.
Finally, a parallelisation scheme is presented, as parallelisation is
unavoidable when studying large scale problems involving several thousands of
simultaneously deforming bodies on hundreds of distributed memory computing
processors
Modelling cell movement and chemotaxis pseudopod based feedback
A computational framework is presented for the simulation of eukaryotic cell migration and chemotaxis. An empirical pattern formation model, based on a system of non-linear reaction-diffusion equations, is approximated on an evolving cell boundary using an Arbitrary Lagrangian Eulerian surface finite element method (ALE-SFEM). The solution state is used to drive a mechanical model of the protrusive and retractive forces exerted on the cell boundary. Movement of the cell is achieved using a level set method. Results are presented for cell migration with and without chemotaxis. The simulated behaviour is compared with experimental results of migrating Dictyostelium discoideum cells
An implicit surface tension model for the analysis of droplet dynamics
A Lagrangian incompressible fluid flow model is extended by including an implicit surface tension term in order to analyze droplet dynamics. The Lagrangian framework is adopted to model the fluid and track its boundary, and the implicit surface tension term is used to introduce the appropriate forces at the domain boundary. The introduction of the tangent matrix corresponding to the surface tension force term ensures enhanced stability of the derived model. Static, dynamic and sessile droplet examples are simulated to validate the model and evaluate its performance. Numerical results are capable of reproducing the pressure distribution in droplets, and the advancing and receding contact angles evolution for droplets in varying substrates and inclined planes. The model is stable even at time steps up to 20 times larger than previously reported in literature and achieves first and second order convergence in time and space, respectively. The present implicit surface tension implementation is applicable to any model where the interface is represented by a moving boundary mesh.Peer ReviewedPostprint (published version
A computational method for the coupled solution of reaction–diffusion equations on evolving domains and manifolds: application to a model of cell migration and chemotaxis
In this paper, we devise a moving mesh finite element method for the approximate solution of coupled bulk–surface reaction–diffusion equations on an evolving two dimensional domain. Fundamental to the success of the method is the robust generation of bulk and surface meshes. For this purpose, we use a novel moving mesh partial differential equation (MMPDE) approach. The developed method is applied to model problems with known analytical solutions; these experiments indicate second-order spatial and temporal accuracy. Coupled bulk–surface problems occur frequently in many areas; in particular, in the modelling of eukaryotic cell migration and chemotaxis. We apply the method to a model of the two-way interaction of a migrating cell in a chemotactic field, where the bulk region corresponds to the extracellular region and the surface to the cell membrane
Mesh update techniques for free-surface flow solvers using spectral element method
This paper presents a novel mesh-update technique for unsteady free-surface
Newtonian flows using spectral element method and relying on the arbitrary
Lagrangian--Eulerian kinematic description for moving the grid. Selected
results showing compatibility of this mesh-update technique with spectral
element method are given
Level Set Jet Schemes for Stiff Advection Equations: The SemiJet Method
Many interfacial phenomena in physical and biological systems are dominated
by high order geometric quantities such as curvature.
Here a semi-implicit method is combined with a level set jet scheme to handle
stiff nonlinear advection problems.
The new method offers an improvement over the semi-implicit gradient
augmented level set method previously introduced by requiring only one
smoothing step when updating the level set jet function while still preserving
the underlying methods higher accuracy. Sample results demonstrate that
accuracy is not sacrificed while strict time step restrictions can be avoided
Hybrid finite difference/finite element immersed boundary method
The immersed boundary method is an approach to fluid-structure interaction that uses a Lagrangian
description of the structural deformations, stresses, and forces along with an Eulerian description of the
momentum, viscosity, and incompressibility of the fluid-structure system. The original immersed boundary
methods described immersed elastic structures using systems of flexible fibers, and even now, most
immersed boundary methods still require Lagrangian meshes that are finer than the Eulerian grid. This
work introduces a coupling scheme for the immersed boundary method to link the Lagrangian and Eulerian
variables that facilitates independent spatial discretizations for the structure and background grid. This
approach employs a finite element discretization of the structure while retaining a finite difference scheme
for the Eulerian variables. We apply this method to benchmark problems involving elastic, rigid, and actively
contracting structures, including an idealized model of the left ventricle of the heart. Our tests include cases
in which, for a fixed Eulerian grid spacing, coarser Lagrangian structural meshes yield discretization errors
that are as much as several orders of magnitude smaller than errors obtained using finer structural meshes.
The Lagrangian-Eulerian coupling approach developed in this work enables the effective use of these coarse
structural meshes with the immersed boundary method. This work also contrasts two different weak forms
of the equations, one of which is demonstrated to be more effective for the coarse structural discretizations
facilitated by our coupling approach
Animating physical phenomena with embedded surface meshes
Accurate computational representations of highly deformable surfaces are indispensable in the fields of computer animation, medical simulation, computer vision, digital modeling, and computational physics. The focus of this dissertation is on the animation of physics-based phenomena with highly detailed deformable surfaces represented by triangle meshes.
We first present results from an algorithm that generates continuum mechanics animations with intricate surface features. This method combines a finite element method with a tetrahedral mesh generator and a high resolution surface mesh, and it is orders of magnitude more efficient than previous approaches. Next, we present an efficient solution for the challenging problem of computing topological changes in detailed dynamic surface meshes. We then introduce a new physics-inspired surface tracking algorithm that is capable of preserving arbitrarily thin features and reproducing realistic fine-scale topological changes like Rayleigh-Plateau instabilities. This physics-inspired surface tracking technique also opens the door for a unique coupling between surficial finite element methods and volumetric finite difference methods, in order to simulate liquid surface tension phenomena more efficiently than any previous method. Due to its dramatic increase in computational resolution and efficiency, this method yielded the first computer simulations of a fully developed crown splash with droplet pinch off.Ph.D.Committee Chair: Turk, Greg; Committee Member: Essa, Irfan; Committee Member: Liu, Karen; Committee Member: Mucha, Peter J.; Committee Member: Rossignac, Jare
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