Diffuse interface models of locally inextensible vesicles in a viscous fluid

We present a new diffuse interface model for the dynamics of inextensible vesicles in a viscous fluid. A new feature of this work is the implementation of the local inextensibility condition in the diffuse interface context. Local inextensibility is enforced by using a local Lagrange multiplier, which provides the necessary tension force at the interface. To solve for the local Lagrange multiplier, we introduce a new equation whose solution essentially provides a harmonic extension of the local Lagrange multiplier off the interface while maintaining the local inextensibility constraint near the interface. To make the method more robust, we develop a local relaxation scheme that dynamically corrects local stretching/compression errors thereby preventing their accumulation. Asymptotic analysis is presented that shows that our new system converges to a relaxed version of the inextensible sharp interface model. This is also verified numerically. Although the model does not depend on dimension, we present numerical simulations only in 2D. To solve the 2D equations numerically, we develop an efficient algorithm combining an operator splitting approach with adaptive finite elements where the Navier-Stokes equations are implicitly coupled to the diffuse interface inextensibility equation. Numerical simulations of a single vesicle in a shear flow at different Reynolds numbers demonstrate that errors in enforcing local inextensibility may accumulate and lead to large differences in the dynamics in the tumbling regime and differences in the inclination angle of vesicles in the tank-treading regime. The local relaxation algorithm is shown to effectively prevent this accumulation by driving the system back to its equilibrium state when errors in local inextensibility arise.Comment: 25 page

A Second Order Fully-discrete Linear Energy Stable Scheme for a Binary Compressible Viscous Fluid Model

We present a linear, second order fully discrete numerical scheme on a staggered grid for a thermodynamically consistent hydrodynamic phase field model of binary compressible fluid flow mixtures derived from the generalized Onsager Principle. The hydrodynamic model not only possesses the variational structure, but also warrants the mass, linear momentum conservation as well as energy dissipation. We first reformulate the model in an equivalent form using the energy quadratization method and then discretize the reformulated model to obtain a semi-discrete partial differential equation system using the Crank-Nicolson method in time. The numerical scheme so derived preserves the mass conservation and energy dissipation law at the semi-discrete level. Then, we discretize the semi-discrete PDE system on a staggered grid in space to arrive at a fully discrete scheme using the 2nd order finite difference method, which respects a discrete energy dissipation law. We prove the unique solvability of the linear system resulting from the fully discrete scheme. Mesh refinements and two numerical examples on phase separation due to the spinodal decomposition in two polymeric fluids and interface evolution in the gas-liquid mixture are presented to show the convergence property and the usefulness of the new scheme in applications

Mathematical modelling in cell migration : tackling biochemistry in changing geometries

Directed cell migration poses a rich set of theoretical challenges. Broadly, these are concerned with 1) how cells sense external signal gradients and adapt; 2) how actin polymerisation is localised to drive the leading cell edge and Myosin-II molecular motors retract the cell rear; and 3) how the combined action of cellular forces and cell adhesion results in cell shape changes and net migration. Reaction-diffusion models for biological pattern formation going back to Turing have long been used to explain generic principles of gradient sensing and cell polarisation in simple, static geometries like a circle. In this minireview we focus on recent research which aims at coupling the biochemistry with cellular mechanics and modelling cell shape changes. In particular we want to contrast two principal modelling approaches, 1) interface tracking where the cell membrane, interfacing cell interior and exterior, is explicitly represented by a set of moving points in 2D or 3D space, and 2) interface capturing. In interface capturing the membrane is implicitly modelled, analogously to a level line in a hilly landscape whose topology changes according to forces acting on the membrane. With the increased availability of high-quality 3D microscopy data of complex cell shapes, such methods will become increasingly important in data-driven, image-based modelling to better understand the mechanochemistry underpinning cell motion

Solving multi-physics problems using adaptive finite elements with independently refined meshes

In this thesis, we study a numerical tool named multi-mesh method within the framework of the adaptive finite element method. The aim of this method is to minimize the size of the linear system to get the optimal performance of simulations. Multi-mesh methods are typically used in multi-physics problems, where more than one component is involved in the system. During the discretization of the weak formulation of partial differential equations, a finite-dimensional space associated with an independently refined mesh is assigned to each component respectively. The usage of independently refined meshes leads less degrees of freedom from a global point of view. To our best knowledge, the first multi-mesh method was presented at the beginning of the 21st Century. Similar techniques were announced by different mathematics researchers afterwards. But, due to some common restrictions, this method is not widely used in the field of numerical simulations. On one hand, only the case of two-mesh is taken into scientists\' consideration. But more than two components are common in multi-physics problems. Each is, in principle, allowed to be defined on an independent mesh. Besides that, the multi-mesh methods presented so far omit the possibility that coefficient function spaces live on the different meshes from the trial and test function spaces. As a ubiquitous numerical tool, the multi-mesh method should comprise the above circumstances. On the other hand, users are accustomed to improving the performance by taking the advantage of parallel resources rather than running simulations with the multi-mesh approach on one single processor, so it would be a pity if such an efficient method was only available in sequential. The multi-mesh method is actually used within local assembling process, which should not be conflict with parallelization. In this thesis, we present a general multi-mesh method without the limitation of the number of meshes used in the system, and it can be applied to parallel environments as well. Chapter 1 introduces the background knowledge of the adaptive finite element method and the pioneering work, on which this thesis is based. Then, the main idea of the multi-mesh method is formally derived and the detailed implementation is discussed in Chapter 2 and 3. In Chapter 4, applications, e.g. the multi-phase flow problem and the dendritic growth, are shown to prove that our method is superior in contrast to the standard single-mesh finite element method in terms of performance, while accuracy is not reduced

Thermodynamically Consistent Hydrodynamic Phase Field Models and Numerical Approximation for Multi-Component Compressible Viscous Fluid Mixtures

Material systems comprising of multi-component, some of which are compressible, are ubiquitous in nature and industrial applications. In the compressible fluid flow, the material compressibility comes from two sources. One is the material compressibility itself and another is the mass-generating source. For example, the compressibility in the binary fluid flows of non-hydrocarbon (e.g. Carbon dioxide) and hydrocarbons encountered in the enhanced oil recovery (EOR) process, comes from the compressibility of the gas-liquid mixture itself. Another example of the mixture of compressible fluids is growing tissue, in which cell proliferation and cell migration make the material volume changes so that it cannot be described as incompressible. We present a systematic derivation of thermodynamically consistent hydrodynamic phase field models for compressible viscous fluid mixtures using the generalized Onsager principle along with the one fluid multi-component formulation. By maintaining momentum conservation while enforcing mass conservation at different levels, we obtain two compressible models. When the fluid components in the mixture are incompressible, we show that one compressible model reduces to the quasi-incompressible model via a Lagrange multiplier approach. Several different approaches to arriving at the quasi-incompressible model are discussed. Then, we conduct a linear stability analysis on all the binary models derived in the thesis and show the differences of the models in near equilibrium dynamics. We present a linear, second order fully discrete numerical scheme on a staggered grid for a thermodynamically consistent hydrodynamic phase field model of binary compressible flows of fluid mixtures derived from the generalized Onsager Principle. v The hydrodynamic model not only possesses the variational structure, but also warrants the mass, linear momentum conservation as well as energy dissipation. We first reformulate the model in an equivalent form using the energy quadratization method and then discretize the reformulated model to obtain a semi-discrete partial differential equation system using the Crank-Nicolson method in time. The numerical scheme so derived preserves the mass conservation and energy dissipation law at the semi-discrete level. Then, we discretize the semi-discrete PDE system on a staggered grid in space to arrive at a fully discrete scheme using the 2nd order finite difference method, which respects a discrete energy dissipation law. We prove the unique solvability of the linear system resulting from the fully discrete scheme. Mesh refinements are presented to show the convergence property of the new scheme. In the compressible polymer mixtures, we first construct a Flory-Huggins type of free energy and explore the phase separation phenomena due to spinodal decomposition. We investigate the phase separation with and without hydrodynamics, respectively. It tells us that hydrodynamics indeed changes local densities, the path of phase evolution and even the final energy steady states of fluid mixtures. This is alarming, indicating that hydrodynamic effects are instrumental in determining the correct spatial phase diagram for the binary fluid mixture. Finally, we study the interface dynamics and investigate the mass adsorption phenomena of one component at the interface, to show the performance of our model and the numerical scheme in simulating hydrodynamics of the hydrocarbon mixture

Diffuse interface models of locally inextensible vesicles in a viscous fluid

We present a new diffuse interface model for the dynamics of inextensible vesicles in a viscous fluid with inertial forces. A new feature of this work is the implementation of the local inextensibility condition in the diffuse interface context. Local inextensibility is enforced by using a local Lagrange multiplier, which provides the necessary tension force at the interface. We introduce a new equation for the local Lagrange multiplier whose solution essentially provides a harmonic extension of the multiplier off the interface while maintaining the local inextensibility constraint near the interface. We also develop a local relaxation scheme that dynamically corrects local stretching/compression errors thereby preventing their accumulation. Asymptotic analysis is presented that shows that our new system converges to a relaxed version of the inextensible sharp interface model. This is also verified numerically. To solve the equations, we use an adaptive finite element method with implicit coupling between the Navier-Stokes and the diffuse interface inextensibility equations. Numerical simulations of a single vesicle in a shear flow at different Reynolds numbers demonstrate that errors in enforcing local inextensibility may accumulate and lead to large differences in the dynamics in the tumbling regime and smaller differences in the inclination angle of vesicles in the tank-treading regime. The local relaxation algorithm is shown to prevent the accumulation of stretching and compression errors very effectively. Simulations of two vesicles in an extensional flow show that local inextensibility plays an important role when vesicles are in close proximity by inhibiting fluid drainage in the near contact region