In this thesis, we will study bio-mathematics. We will introduce differential equations, biological applications, and simulations with emphasis in molecular events. One of the first courses of action is to introduce and construct a mathematical model of our biological element. The biological element of study is the Hepatitis C virus. The idea in creating a mathematical model is to approach the biological element in small steps. We will first introduce a block (schematic) diagram of the element, create differential equations that define the diagram, convert the dimensional equations to non-dimensional equations, reduce the number of parameters, identify the important parameters, and analyze the results. These results will tell us which variables must be adjusted to prevent the Hepatitis C virus from becoming chronic.

Meshless methods are a relatively new class of schemes for the numerical solution of partial differential equations. Their special characteristic is that they do not require a mesh but only need a distribution of points in the computational domain. The approximation at any point of spatial derivatives appearing in the partial differential equations is performed using a local cloud of points called the "connectivity" (or stencil). A point distribution can be more easily generated than a grid since we have less constraints to satisfy. The present work uses two meshless methods; an existing scheme called Least Squares Kinetic Upwind Method (LSKUM) and a new scheme called Kinetic Meshless Method (KMM). LSKUM is a "kinetic" scheme which uses a "least squares" approximation} for discretizing the derivatives occurring in the partial differential equations. The first part of the thesis is concerned with some theoretical properties and application of LSKUM to 3-D point distributions. Using previously established results we show that first order LSKUM in 1-D is positivity preserving under a CFL-like condition. The 3-D LSKUM is applied to point distributions obtained from FAME mesh. FAME, which stands for Feature Associated Mesh Embedding, is a composite overlapping grid system developed at QinetiQ (formerly DERA), UK, for store separation problems. The FAME mesh has a cell-based data structure and this is first converted to a node-based data structure which leads to a point distribution. For each point in this distribution we find a set of nearby nodes which forms the connectivity. The connectivity at each point (which is also the "full stencil" for that point) is split along each of the three coordinate directions so that we need six split (or half or one-sided) stencils at each point. The split stencils are used in LSKUM to calculate the split-flux derivatives arising in kinetic schemes which gives the upwind character to LSKUM. The "quality" of each of these stencils affects the accuracy and stability of the numerical scheme. In this work we focus on developing some numerical criteria to quantify the quality of a stencil for meshless methods like LSKUM. The first test is based on singular value decomposition of the over-determined problem and the singular values are used to measure the ill-conditioning (generally caused by a flat stencil). If any of the split stencils are found to be ill-conditioned then we use the full stencil for calculating the corresponding split flux derivative. A second test that is used is based on an accuracy measurement. The idea of this test is that a "good" stencil must give accurate estimates of derivatives and vice versa. If the error in the computed derivatives is above some specified tolerance the stencil is classified as unacceptable. In this case we either enhance the stencil (to remove disc-type degenerate structure) or switch to full stencil. It is found that the full stencil almost always behaves well in terms of both the tests. The use of these two tests and the associated modifications of defective stencils in an automatic manner allows the solver to converge without any blow up. The results obtained for a 3-D configuration compare favorably with wind tunnel measurements and the framework developed here provides a rational basis for approaching the connectivity selection problem. The second part of the thesis deals with a new scheme called Kinetic Meshless Method (KMM) which was developed as a consequence of the experience obtained with LSKUM and FAME mesh. As mentioned before the full stencil is generally better behaved than the split stencils. Hence the new scheme is constructed so that it does not require split stencils but operates on a full stencil (which is like a centered stencil). In order to obtain an upwind bias we introduce mid-point states (between a point and its neighbour) and the least squares fitting is performed using these mid-point states. The mid-point states are defined in an upwind-biased manner at the kinetic/Boltzmann level and moment-method strategy leads to an upwind scheme at the Euler level. On a standard 4-point Cartesian stencil this scheme reduces to finite volume method with KFVS fluxes. We can also show the rotational invariance of the scheme which is an important property of the governing equations themselves. The KMM is extended to higher order accuracy using a reconstruction procedure similar to finite volume schemes even though we do not have (or need) any cells in the present case. Numerical studies on a model 2-D problem show second order accuracy. Some theoretical and practical advantages of using a kinetic formulation for deriving the scheme are recognized. Several 2-D inviscid flows are solved which also demonstrate many important characteristics. The subsonic test cases show that the scheme produces less numerical entropy compared to LSKUM, and is also better in preserving the symmetry of the flow. The test cases involving discontinuous flows show that the new scheme is capable of resolving shocks very sharply especially with adaptation. The robustness of the scheme is also very good as shown in the supersonic test cases.

Title: Non-newtonian fluid flow simulation using lattice Boltzmann method Author: Bc. Pavel Kuriščák Department: Mathematical Institute, Charles University Supervisor: RNDr. Ing. Jaroslav Hron Ph.D. Supervisor's e-mail address: Jaroslav.Hron@mff.cuni.cz Abstract: The aim of this thesis is to find and estabilish a modification to the Lattice Boltzmann Method, allowing it to simulate non-newtonian behaviour of fluids. In the theoretical part of thesis, there is introduced a derivation, based on the work of [22], that is capable of arriving to macroscopical Navier-Stokes equa- tions completely a priori from the Boltzmann equation, utilizing the Hermite basis expansion. This derivation is afterwards applied to the method suggested by [11], that uses the changed equilibrium distribution to fine-tune the local fluid viscosity according to the non-newtonian model. In the last part of thesis, this method is implemented in the form of lattice kinetic scheme and tested on three sample problems. Keywords: Lattice Boltzmann Method, non-newtonian fluids, Hermite expansion, lattice kinetic scheme