We introduce a new troubled-cell indicator for the discontinuous Galerkin (DG) methods for solving hyperbolic conservation laws. This indicator can be defined on unstructured meshes for high order DG methods and depends only on data from the target cell and its immediate neighbors. It is able to identify shocks without PDE sensitive parameters to tune. Extensive one- and two-dimensional simulations on the hyperbolic systems of Euler equations indicate the good performance of this new troubled-cell indicator coupled with a simple minmod-type TVD limiter for the Runge-Kutta DG (RKDG) methods.

Most biochemical processes involve macromolecules in solution. The corresponding electrostatics is of central importance for understanding their structures and functions. An accurate and efficient numerical scheme is introduced to evaluate the corresponding electrostatic potential and force by solving the governing Poisson-Boltzmann equation. This paper focuses on the following issues: (i) the point charge singularity problem, (ii) the dielectric discontinuity problem across a molecular surface, and (iii) the infinite domain problem. Green's function associated with the point charges plus a harmonic function is introduced as the zeroth order approximation to the solution to solve the point charge singularity problem. A jump condition capturing finite difference scheme is adopted to solve the discontinuity problem across molecule surfaces, where a body-fitting grid is used. The infinite domain problem is solved by mapping the outer infinite domain into a finite domain. The corresponding stiffness matrix is symmetric and positive definite, therefore, fast algorithm such as preconditioned conjugate gradient method can be applied for inner iteration. Finally, the resulting scheme is second order accurate for both the potential and its gradient.

Peskin's Immersed Boundary (IB) method is one of the most popular numerical methods for many years and has been applied to problems in mathematical biology, fluid mechanics, material sciences, and many other areas. Peskiness IB method is associated with discrete delta functions. It is believed that the IB method is first order accurate in the $L^{\infty}$ norm. But almost no rigorous proof could be found in the literature until recently [Mori, Comm. Pure. Appl. Math: 61:2008] in which the author showed that the velocity is indeed first order accurate for the Stokes equations with a periodic boundary condition. In this paper, we show first order convergence with a $\log h$ factor of the IB method for elliptic interface problems with Dirichlet boundary conditions.

To avoid the order reduction when third order implicit-explicit Runge-Kutta time discretization is used together with the local discontinuous Galerkin (LDG) spatial discretization, for solving convection-diffusion problems with time-dependent Dirichlet boundary conditions, we propose a strategy of boundary treatment at each intermediate stage in this paper. The proposed strategy can achieve optimal order of accuracy by numerical verification. Also by suitably setting numerical flux on the boundary in the LDG methods, and by establishing an important relationship between the gradient and interface jump of the numerical solution with the independent numerical solution of the gradient and the given boundary conditions, we build up the unconditional stability of the corresponding scheme, in the sense that the time step is only required to be upper bounded by a suitable positive constant, which is independent of the mesh size.

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