Plasmas in modern tokamak experiments contain a significant fraction of impurity ion species in addition to main deuterium background. A new unlike-particle collision operator for δf particle simulation has been developed to study the nonlocal effects of impurities due to finite ion orbits on neoclassical transport in toroidal plasmas. A new algorithm for simulation of cross-collisions between different ion species includes test-particle and conserving field-particle operators. An improved field-particle operator is designed to exactly enforce conservation of number, momentum and energy.

A discontinuous Galerkin method for the ideal 5 moment two-fluid plasma system is presented. The method uses a second or third order discontinuous Galerkin spatial discretization and a third order TVD Runge-Kutta time stepping scheme. The method is benchmarked against an analytic solution of a dispersive electron acoustic square pulse as well as the two-fluid electromagnetic shock [1] and existing numerical solutions to the GEM challenge magnetic reconnection problem [2]. The algorithm can be generalized to arbitrary geometries and three dimensions. An approach to maintaining small gauge errors based on error propagation is suggested.

The simulation of multiphase flows is an outstanding challenge, due to the inherent complexity of the underlying physical phenomena and to the fact that multiphase flows are very diverse in nature, and so are the laws governing their dynamics. In the last two decades, a new class of mesoscopic methods, based on minimal lattice formulation of Boltzmann kinetic equation, has gained significant interest as an efficient alternative to continuum methods based on the discretization of the NS equations for non ideal fluids. In this paper, three different multiphase models based on the lattice Boltzmann method (LBM) are discussed, in order to assess the capability of the method to deal with multiphase flows on a wide spectrum of operating conditions and multiphase phenomena. In particular, the range of application of each method is highlighted and its effectiveness is qualitatively assessed through comparison with numerical and experimental literature data.

A robust and efficient solver coupling computational fluid dynamics (CFD) with discrete element method (DEM) is developed to simulate particle-laden flows in various physical settings. An interpolation algorithm suitable for unstructured meshes is proposed to translate between mesh-based Eulerian fields and particle-based Lagrangian quantities. The interpolation scheme reduces the mesh-dependence of the averaging and interpolation procedures. In addition, the fluid-particle interaction terms are treated semi-implicitly in this algorithm to improve stability and to maintain accuracy. Finally, it is demonstrated that sub-stepping is desirable for fluid-particle systems with small Stokes numbers. A momentum-conserving sub-stepping technique is introduced into the fluid-particle coupling procedure, so that problems with a wide range of time scales can be solved without resorting to excessively small time steps in the CFD solver. Several numerical examples are presented to demonstrate the capabilities of the solver and the merits of the algorithm.

We design stable and high-order accurate finite volume schemes for the ideal MHD equations in multi-dimensions. We obtain excellent numerical stability due to some new elements in the algorithm. The schemes are based on three- and five-wave approximate Riemann solvers of the HLL-type, with the novelty that we allow a varying normal magnetic field. This is achieved by considering the semi-conservative Godunov-Powell form of the MHD equations. We show that it is important to discretize the Godunov-Powell source term in the right way, and that the HLL-type solvers naturally provide a stable upwind discretization. Second-order versions of the ENO- and WENO-type reconstructions are proposed, together with precise modifications necessary to preserve positive pressure and density. Extending the discrete source term to second order while maintaining stability requires non-standard techniques, which we present. The first- and second-order schemes are tested on a suite of numerical experiments demonstrating impressive numerical resolution as well as stability, even on very fine meshes.

A reconstruction-based discontinuous Galerkin method is presented for the solution of the compressible Navier-Stokes equations on arbitrary grids. In this method, an in-cell reconstruction is used to obtain a higher-order polynomial representation of the underlying discontinuous Galerkin polynomial solution and an inter-cell reconstruction is used to obtain a continuous polynomial solution on the union of two neighboring, interface-sharing cells. The in-cell reconstruction is designed to enhance the accuracy of the discontinuous Galerkin method by increasing the order of the underlying polynomial solution. The inter-cell reconstruction is devised to remove an interface discontinuity of the solution and its derivatives and thus to provide a simple, accurate, consistent, and robust approximation to the viscous and heat fluxes in the Navier-Stokes equations. A parallel strategy is also devised for the resulting reconstruction discontinuous Galerkin method, which is based on domain partitioning and Single Program Multiple Data (SPMD) parallel programming model. The RDG method is used to compute a variety of compressible flow problems on arbitrary meshes to demonstrate its accuracy, efficiency, robustness, and versatility. The numerical results demonstrate that this RDG method is third-order accurate at a cost slightly higher than its underlying second-order DG method, at the same time providing a better performance than the third order DG method, in terms of both computing costs and storage requirements.

We use the recently proposed Nested Stochastic Simulation Algorithm (Nested SSA) to simulate the cell cycle model for budding yeast. The results show that Nested SSA is able to significantly reduce the computational cost while capturing the essential dynamical features of the system.

In this paper, we model laser-gas interactions and propagation in some extreme regimes. After a mathematical study of a micro-macro Maxwell-Schrödinger model [1] for short, high-frequency and intense laser-gas interactions, we propose to improve this model by adding a plasma equation in order to precisely take into account free electron effects. We examine if such a model can predict and explain complex structures such as filaments, on a physical and numerical basis. In particular, we present in this paper a first numerical observation of nonlinear focusing effects using an ab-initio gas representation and linking our results with existing nonlinear models.

This paper presents a novel high-order space-time method for hyperbolic conservation laws. Two important concepts, the staggered space-time mesh of the space-time conservation element/solution element (CE/SE) method and the local discontinuous basis functions of the space-time discontinuous Galerkin (DG) finite element method, are the two key ingredients of the new scheme. The staggered space-time mesh is constructed using the cell-vertex structure of the underlying spatial mesh. The universal definitions of CEs and SEs are independent of the underlying spatial mesh and thus suitable for arbitrarily unstructured meshes. The solution within each physical time step is updated alternately at the cell level and the vertex level. For this solution updating strategy and the DG ingredient, the new scheme here is termed as the discontinuous Galerkin cell-vertex scheme (DG-CVS). The high order of accuracy is achieved by employing high-order Taylor polynomials as the basis functions inside each SE. The present DG-CVS exhibits many advantageous features such as Riemann-solver-free, high-order accuracy, point-implicitness, compactness, and ease of handling boundary conditions. Several numerical tests including the scalar advection equations and compressible Euler equations will demonstrate the performance of the new method.