Implicit and Implicit-Explicit Strong Stability Preserving Runge-Kutta Methods with High Linear Order

When evolving in time the solution of a hyperbolic partial differential equation, it is often desirable to use high order strong stability preserving (SSP) time discretizations. These time discretizations preserve the monotonicity properties satisfied by the spatial discretization when coupled with the first order forward Euler, under a certain time-step restriction. While the allowable time-step depends on both the spatial and temporal discretizations, the contribution of the temporal discretization can be isolated by taking the ratio of the allowable time-step of the high order method to the forward Euler time-step. This ratio is called the strong stability coefficient. The search for high order strong stability time-stepping methods with high order and large allowable time-step had been an active area of research. It is known that implicit SSP Runge-Kutta methods exist only up to sixth order. However, if we restrict ourselves to solving only linear autonomous problems, the order conditions simplify and we can find implicit SSP Runge-Kutta methods of any linear order. In the current work we aim to find very high linear order implicit SSP Runge-Kutta methods that are optimal in terms of allowable time-step. Next, we formulate an optimization problem for implicit-explicit (IMEX) SSP Runge-Kutta methods and find implicit methods with large linear stability regions that pair with known explicit SSP Runge-Kutta methods of orders plin=3,4,6 as well as optimized IMEX SSP Runge-Kutta pairs that have high linear order and nonlinear orders p=2,3,4. These methods are then tested on sample problems to verify order of convergence and to demonstrate the sharpness of the SSP coefficient and the typical behavior of these methods on test problems

Optimized explicit Runge-Kutta schemes for the spectral difference method applied to wave propagation problems

Explicit Runge-Kutta schemes with large stable step sizes are developed for integration of high order spectral difference spatial discretization on quadrilateral grids. The new schemes permit an effective time step that is substantially larger than the maximum admissible time step of standard explicit Runge-Kutta schemes available in literature. Furthermore, they have a small principal error norm and admit a low-storage implementation. The advantages of the new schemes are demonstrated through application to the Euler equations and the linearized Euler equations.Comment: 37 pages, 3 pages of appendi

Extrapolation-Based Implicit-Explicit Peer Methods with Optimised Stability Regions

In this paper we investigate a new class of implicit-explicit (IMEX) two-step methods of Peer type for systems of ordinary differential equations with both non-stiff and stiff parts included in the source term. An extrapolation approach based on already computed stage values is applied to construct IMEX methods with favourable stability properties. Optimised IMEX-Peer methods of order p = 2, 3, 4, are given as result of a search algorithm carefully designed to balance the size of the stability regions and the extrapolation errors. Numerical experiments and a comparison to other implicit-explicit methods are included.Comment: 21 pages, 6 figure

A Continuum Poisson-Boltzmann Model for Membrane Channel Proteins

Membrane proteins constitute a large portion of the human proteome and perform a variety of important functions as membrane receptors, transport proteins, enzymes, signaling proteins, and more. The computational studies of membrane proteins are usually much more complicated than those of globular proteins. Here we propose a new continuum model for Poisson-Boltzmann calculations of membrane channel proteins. Major improvements over the existing continuum slab model are as follows: 1) The location and thickness of the slab model are fine-tuned based on explicit-solvent MD simulations. 2) The highly different accessibility in the membrane and water regions are addressed with a two-step, two-probe grid labeling procedure, and 3) The water pores/channels are automatically identified. The new continuum membrane model is optimized (by adjusting the membrane probe, as well as the slab thickness and center) to best reproduce the distributions of buried water molecules in the membrane region as sampled in explicit water simulations. Our optimization also shows that the widely adopted water probe of 1.4 {\AA} for globular proteins is a very reasonable default value for membrane protein simulations. It gives an overall minimum number of inconsistencies between the continuum and explicit representations of water distributions in membrane channel proteins, at least in the water accessible pore/channel regions that we focus on. Finally, we validate the new membrane model by carrying out binding affinity calculations for a potassium channel, and we observe a good agreement with experiment results.Comment: 40 pages, 6 figures, 5 table