Thesis(M.S.)--Auburn University, 2005. / Abstract. Vita. Includes bibliographic references.

We present the application of the boundary integral equation method for solving the motion of biological cell or particle under Stokes flow in the presence of electrostatic field. The huge dense matrix-vector product from the boundary integral method poses a computationally challenging problem for solving the large system of equations generated. In our work, we used the precorrected-FFT (pFFT) method to reduce the computational time and memory usage drastically, so that large scale simulations can be performed quickly on a personal computer. Results on the force field acting on the particle, as well as the behavior of the particle through cell trap are presented. / Singapore-MIT Alliance (SMA)

Mixing in Stokes flows is notoriously difficult to achieve. With characteristic scales of the flows being too small for the turbulence to be present, and too large for the molecular diffusion to be significant, the chaotic advection presents almost the only mechanism that can lead to mixing. Unfortunately for mixing, the intrinsic symmetries of the flow create invariant surfaces that act as barriers to mixing. Thus, a key to efficient mixing is to add to the original (symmetric) flow a certain kind of perturbation that destroys those symmetries. In this dissertation, two ways of obtaining mixing in 3D near-integrable bounded time -dependent Stoke Flows are studied: resonances and separatrix crossings. First, I illustrate that the resonances between different components of the original flow and the perturbation may break the invariant surfaces, paving a way to the large-scale mixing. Theoretical estimations are compared against the results of numerical simulations, as well as 3D particle tracking velocimetry (3D-PTV) experimental results. Second, chaotic advection and mixing due to quasi-random jumps of the adiabatic invariant (AI) occurring when a streamline crosses the separatrix surfaces is studied. Analytical expressions for the change in the AI near the separatrix surfaces are derived and compared with numerical simulations. / Mechanical Engineering

Since it is difficult or impossible to generate turbulent flow in a highly viscous fluid or a microfluidic system, efficient mixing becomes a challenge. However, it is possible in a laminar flow to generate chaotic particle trajectories (well-known as chaotic advection), that can lead to effective mixing. This dissertation studies mixing in flows with the limiting case of zero Reynolds numbers that are called Stokes flows and illustrates the practical use of different theories, namely the topological chaos theory, the set-oriented analysis and lobe dynamics in the analysis, design and optimization of different laminar-flow mixing systems. In a recent development, the topological chaos theory has been used to explain the chaos built in the flow only based on the topology of boundary motions. Without considering any details of the fluid dynamics, this novel method uses the Thurston-Nielsen (TN) classification theorem to predict and describe the stretching of material lines both qualitatively and quantitatively. The practical application of this theory toward design and optimization of a viscous-flow mixer and the important role of periodic orbits as "ghost rods" are studied. The relationship between stretching of material lines (chaos) and the homogenization of a scalar (mixing) in chaotic Stokes flows is examined in this work. This study helps determining the extent to which the stretching can represent real mixing. Using a set-oriented approach to describe the stirring in the flow, invariance or leakiness of the Almost Invariant Sets (AIS) playing the role of ghost rods is found to be in a direct relationship with the rate of homogenization of a scalar. The mixing caused by these AIS and the variations of their structure are explained from the point of view of geometric mechanics using transport through lobes. These lobes are made of segments of invariant manifolds of the periodic points that are generators of the ghost rods. A variety of the concentration-based measures, the important parameters of their calculation, and the implicit effect of diffusion are described. The studies, measures and methods of this dissertation help in the evaluation and understanding of chaotic mixing systems in nature and in industrial applications. They provide theoretical and numerical grounds for selection of the appropriate mixing protocol and design and optimization of mixing systems, examples of which can be seen throughout the dissertation. / Ph. D.

In this thesis, three parts, each with several chapters, are respectively devoted to hydrostatic, viscous and inertial fluids theories and applications. In the hydrostatics part, the classical Maclaurin spheroids theory is generalized, for the first time, to a more realistic multi-layer model, which enables the studies of some gravity problems and direct numerical simulations of flows in fast rotating spheroidal cavities. As an application of the figure theory, the zonal flow in the deep atmosphere of Jupiter is investigated for a better understanding of the Jovian gravity field. High viscosity flows, for example Stokes flows, occur in a lot of processes involving low-speed motions in fluids. Microorganism swimming is such typical a case. A fully three dimensional analytic solution of incompressible Stokes equation is derived in the exterior domain of an arbitrarily translating and rotating prolate spheroid, which models a large family of microorganisms such as cocci bacteria. The solution is then applied to the magnetotactic bacteria swimming problem and good consistency has been found between theoretical predictions and laboratory observations of the moving patterns of such bacteria under magnetic fields. In the analysis of dynamics of planetary fluid systems, which are featured by fast rotation and very small viscosity effects, three dimensional fully nonlinear numerical simulations of Navier-Stokes equations play important roles. A precession driven flow in a rotating channel is studied by the combination of asymptotic analyses and fully numerical simulations. Various results of laminar and turbulent flows are thereby presented. Computational fluid dynamics requires massive computing capability. To make full use of the power of modern high performance computing facilities, a C++ finite-element analysis code is under development based on PETSc platform. The code and data structures will be elaborated, along with the presentations of some preliminary results.

The research presented in this thesis was motivated by the desire to understand the flow field within a new digital microfluidic device currently under development. This required an investigation of the dynamics of a droplet migrating along the surface of another fluid due to interfacial surface tension gradients. The quantitative analysis of the flow field presented in this thesis provides the first known solution for the velocity field in a migrating droplet confined to an interface. The first step towards gaining insight into the flow field was accomplished by using the method of reflections to obtain an analytical model for a submerged droplet migrating near a free surface. The submerged droplet model enabled the analysis of the velocity field and droplet migration speed and their dependence on the fluid properties. In general, the migration velocity of a submerged droplet was found to differ dramatically from the classic problem of thermocapillary migration in an unbounded substrate. A boundary-collocation scheme was developed to determine the flow field and migration velocity of a droplet floating trapped at the air-substrate interface. The numerical method was found to produce accurate solutions for the velocity and temperature fields for nearly all parameters. This numerical scheme was used to judge the accuracy of the flow field obtained by the submerged droplet model. In particular, the model was tested using parameter values taken from a digital microfluidic device. It was determined that the submerged droplet model captured most of the flow structure within the microfluidic droplet. However, for a slightly different choice of parameters, agreement between the two methods was lost. In this case, the numerical scheme was used to uncover novel flow structures.

We present a level-set algorithm for topology optimisation and demonstrate its capabilities and advantages in a variety of settings. The algorithm uses discrete element densities so that interpolation schemes are avoided and the boundary of the design is always well defined. A review of the level-set method for topology optimisation, and a description of the mathematical concepts behind the level-set algorithm are given in the introductory chapters. A compact Matlab implementation of the algorithm provides explicit implementation details for the simple example of compliance minimisation with a volume constraint. The remainder of the thesis presents original results obtained using the level-set algorithm. As a new application, we use topology optimisation to maximise fracture resistance. Fracture resistance is assumed to be related to the elastic energy released by a crack propagating in a normal direction from parts of the boundary that are in tension. We develop a suitable fracture resistance objective functional, derive its shape derivative and apply the level-set algorithm to simple examples. Topology optimisation methods that involve intermediate density elements are not suitable to solve this problem because the boundary of the design is not well defined. Our results indicate that the algorithm correctly optimises for fracture resistance. As the method is computationally intensive, we suggest simpler objective functionals that could be used as a proxy for fracture resistance. For example, a perimeter penalty could be added to the compliance objective functional in conjunction with a non-linear elasticity law where the Young's modulus in tension is lower than in compression. The level-set method has only recently been applied to fluid flow problems. We utilise the level-set algorithm to minimise energy dissipation in Stokes flows in both two and three dimensions. The discrete element densities allow the no-slip boundary condition to be applied directly. The Stokes equations therefore need only be solved in the fluid region of the design: this results in significant computational savings compared to conventional material distribution approaches. In order to quantify the computational savings the optimisation problems are resolved using an interpolation scheme to simulate the no-slip boundary condition. This significant advantage of the level-set method for fluid flow problems has not been noted by other authors. The algorithm produces results consistent with those obtained by other topology optimisation approaches, and solves large-scale three dimensional problems with modest computational cost. The first examples of three dimensional periodic microstructure design with the level-set method are presented in this thesis. The level-set algorithm is extended to deal with multiple constraints. This is needed so that materials can be designed with symmetry requirements imposed on their effective properties. To demonstrate the capabilities of the approach, unit cells are designed separately to maximise conductivity and bulk modulus with an isotropy requirement. The resulting materials have properties very close to the relevant Hashin-Shtrikman bounds. The algorithm is then applied to multifunctional material design: unit cells are designed to give isotropic materials that have maximum bulk modulus and maximum conductivity. Cross-property bounds indicate the near-optimality of the microstructures obtained. The design space of the problem is extensively explored with different coefficients of the conductivity and bulk modulus in the objective and different volume constraints. We hypothesise the existence of theoretically optimal single-scale microstructures with the topologies of the computationally optimised microstructures we have found. Structures derived from the Schwartz primitive (P) and diamond (D) minimal surfaces have previously been presented as good multifunctional composites. These structures are elastically anisotropic. Although they have similar conductivity, they have stiffness properties inferior to several of the isotropic optimised microstructures.

We present a level-set algorithm for topology optimisation and demonstrate its capabilities and advantages in a variety of settings. The algorithm uses discrete element densities so that interpolation schemes are avoided and the boundary of the design is always well defined. A review of the level-set method for topology optimisation, and a description of the mathematical concepts behind the level-set algorithm are given in the introductory chapters. A compact Matlab implementation of the algorithm provides explicit implementation details for the simple example of compliance minimisation with a volume constraint. The remainder of the thesis presents original results obtained using the level-set algorithm. As a new application, we use topology optimisation to maximise fracture resistance. Fracture resistance is assumed to be related to the elastic energy released by a crack propagating in a normal direction from parts of the boundary that are in tension. We develop a suitable fracture resistance objective functional, derive its shape derivative and apply the level-set algorithm to simple examples. Topology optimisation methods that involve intermediate density elements are not suitable to solve this problem because the boundary of the design is not well defined. Our results indicate that the algorithm correctly optimises for fracture resistance. As the method is computationally intensive, we suggest simpler objective functionals that could be used as a proxy for fracture resistance. For example, a perimeter penalty could be added to the compliance objective functional in conjunction with a non-linear elasticity law where the Young's modulus in tension is lower than in compression. The level-set method has only recently been applied to fluid flow problems. We utilise the level-set algorithm to minimise energy dissipation in Stokes flows in both two and three dimensions. The discrete element densities allow the no-slip boundary condition to be applied directly. The Stokes equations therefore need only be solved in the fluid region of the design: this results in significant computational savings compared to conventional material distribution approaches. In order to quantify the computational savings the optimisation problems are resolved using an interpolation scheme to simulate the no-slip boundary condition. This significant advantage of the level-set method for fluid flow problems has not been noted by other authors. The algorithm produces results consistent with those obtained by other topology optimisation approaches, and solves large-scale three dimensional problems with modest computational cost. The first examples of three dimensional periodic microstructure design with the level-set method are presented in this thesis. The level-set algorithm is extended to deal with multiple constraints. This is needed so that materials can be designed with symmetry requirements imposed on their effective properties. To demonstrate the capabilities of the approach, unit cells are designed separately to maximise conductivity and bulk modulus with an isotropy requirement. The resulting materials have properties very close to the relevant Hashin-Shtrikman bounds. The algorithm is then applied to multifunctional material design: unit cells are designed to give isotropic materials that have maximum bulk modulus and maximum conductivity. Cross-property bounds indicate the near-optimality of the microstructures obtained. The design space of the problem is extensively explored with different coefficients of the conductivity and bulk modulus in the objective and different volume constraints. We hypothesise the existence of theoretically optimal single-scale microstructures with the topologies of the computationally optimised microstructures we have found. Structures derived from the Schwartz primitive (P) and diamond (D) minimal surfaces have previously been presented as good multifunctional composites. These structures are elastically anisotropic. Although they have similar conductivity, they have stiffness properties inferior to several of the isotropic optimised microstructures.

MSc (Applied Mathematics) / Mathematics and Applied Mathematics Department / In this study the iteration of boundary conditions method (Chizhonkov and Kargin, 2006) is used together with the well known Finite difference numerical method to solve the Stokes problem over a rectangular domain as well as in irregular domain. The iteration of boundary conditions method has been applied to the Stokes problem in a rectangular domain, 􀀀 2 <x< 2 , 􀀀 d 2 < y < d 2 , by the above mentioned researchers. Our main task here is to validate the results of the approximate methods by this analytical method in case of the rectangular domain and extend that to the case of irregular domain.The (Chizhonkov and Kargin, 2006) algorithm is typically the best choice for validation purposes because of its high accuracy. It is known in literature that increasing the parameter d, which represents the ratio of the sides, leads to slow down in convergence of the approximate methods like the conjugate Gradients of Uzawa (Kobelkov and Olshanskii, 2000). It is therefore important that an algorithm that converges uniformly with respect to the parameter d is considered. The (Chizhonkov and Kargin, 2006) algorithm is typical of such an algorithm, and hence our choice of the method in this work. In this project the non-homogeneous Stokes problem is transformed into a homogeneous Stokes problem and the resulting problem is then decomposed into two sub problems that are solvable by the eigenfunction expansion method. Once all necessary coefficients of the generalised Fourier series are known and the functions describing the boundary conditions are prescribed and represented in terms of the Fourier series, we then proceed to formulate the iteration of boundary conditions numerical algorithm. Finally we develop a numerical scheme, using the finite difference methods, for solving the problem in both rectangular and irregular domains. Coding of the numerical algorithm is done using MATLAB 9.0,R2016a programming language, and implemented by the author. The results of the two methods in both cases of boundary conditions are then compared for validation of our purely numerical results. / NRF

A new spline space, the hierarchical structure-preserving B-spline space, is introduced and implemented in the analysis of Stokes flow. The space, when properly constrained, is shown to be stable and to have at least optimal convergence rates in the velocity field and suboptimal convergence rates in the pressure field. However, results show that superoptimal convergence can often be expected in the pressure field, likely due to error reduction in the velocity field. Like other hierarchical spline spaces, these splines are shown to greatly increase accuracy and to drastically lower computation times for analyses on domains whose solution fields have singularities or could otherwise benefit from local refinement. With the advent of this adaptive, locally-refineable, high-fidelity technology, isogeometric methods can become more feasible for use in fluid analyses.