For a class of convection-diffusion equations with variable diffusivity, we construct third order accurate discontinuous Galerkin (DG) schemes on both one and two dimensional rectangular meshes. The DG method with an explicit time stepping can well be applied to nonlinear convection–diffusion equations. It is shown that under suitable time step restrictions, the scaling limiter proposed in Liu and Yu (2014) [23]when coupled with the present DG schemes preserves the solution bounds indicated by the initial data, i.e., the maximum principle, while maintaining uniform third order accuracy. These schemes can be extended to rectangular meshes in three dimension. The crucial for all model scenarios is that an effective test set can be identified to verify the desired bounds of numerical solutions. This is achieved mainly by taking advantage of the flexible form of the diffusive flux and the adaptable decomposition of weighted cell averages. Numerical results are presented to validate the numerical methods and demonstrate their effectiveness.

In this paper, we adapt a simple weighted essentially non-oscillatory (WENO) limiter, originally designed for discontinuous Galerkin (DG) schemes, to the correction procedure via reconstruction (CPR) framework for solving conservation laws. The objective of this simple WENO limiter is to simultaneously maintain uniform high order accuracy of the CPR framework in smooth regions and control spurious numerical oscillations near discontinuities. The WENO limiter we adopt in this paper is particularly simple to implement and will not harm the conservativeness of the CPR framework. Also, it uses information only from the target cell and its immediate neighbors, thus can maintain the compactness of the CPR framework. Since the CPR framework with the WENO limiter does not in general preserve positivity of the solution, we also extend the positivity preserving limiters to the CPR framework. Numerical results in one and two dimensions are provided to illustrate the good behavior of this procedure.

Partial differential equations (PDE) on manifolds arise in many areas, including mathematics and many applied fields. Due to the complicated geometrical structure of the manifold, it is difficult to get efficient numerical method to solve PDE on manifold. In the paper, we propose a method called point integral method (PIM) to solve the Poisson-type equations from point clouds. Among different kinds of PDEs, the Poisson-type equations including the standard Poisson equation and the related eigenproblem of the Laplace-Beltrami operator are one of the most important. In PIM, the key idea is to derive the integral equations which approximates the Poisson-type equations and contains no derivatives but only the values of the unknown function. This feature makes the integral equation easy to be discretized from point cloud. In the paper, we explain the derivation of the integral equations, describe the point integral method and its implementation, and present the numerical experiments to demonstrate the convergence of PIM.

Ligand-receptor binding and unbinding are fundamental biomolecular processes and particularly essential to drug efficacy. Environmental water fluctuations, however, impact the corresponding thermodynamics and kinetics and thereby challenge theoretical descriptions. Here, we devise a holistic, implicit-solvent, multi-method approach to predict the (un)binding kinetics for a generic ligand-pocket model. We use the variational implicit-solvent model (VISM) to calculate the solute-solvent interfacial structures and the corresponding free energies, and combine the VISM with the string method to obtain the minimum energy paths and transition states between the various metastable (“dry” and “wet”) hydration states. The resulting dry-wet transition rates are then used in a spatially-dependent multi-state continuous-time Markov chain Brownian dynamics simulations, and the related Fokker–Planck equation calculations, of the ligand stochastic motion, providing the mean first-passage times for binding and unbinding. We find the hydration transitions to significantly slow down the binding process, in semi-quantitative agreement with existing explicit-water simulations, but significantly accelerate the unbinding process. Moreover, our methods allow the characterization of non-equilibrium hydration states of pocket and ligand during the ligand movement, for which we find substantial memory and hysteresis effects for binding versus unbinding. Our study thus provides a significant step forward towards efficient, physics-based interpretation and predictions of the complex kinetics in realistic ligand-receptor systems.

We propose a simple fast spectral method for the Boltzmann collision operator with general collision kernels. In contrast to the direct spectral method [L. Pareschi and G. Russo, SIAM J. Numer. Anal., 37 (2000), pp. 1217–1245; I. M. Gamba and S. H. Tharkabhushanam, J. Comput. Phys., 228 (2009), pp. 2012–2036], which requires O(N6) memory to store precomputed weights and has O(N6) numerical complexity, the new method has complexity O(MN4 log N), where N is the number of discretization points in each of the three velocity dimensions and M is the total number of discretization points on the sphere and M ≪ N2. Furthermore, it requires no precomputation for the variable hard sphere model and only O(MN4) memory to store precomputed functions for more general collision kernels. Although a faster spectral method is available [C. Mouhot and L. Pareschi, Math. Comp., 75 (2006), pp. 1833–1852] (with complexity O(MN3 logN)), it works only for hard sphere molecules, thus limiting its use for practical problems. Our new method, on the other hand, can apply to arbitrary collision kernels. A series of numerical tests is performed to illustrate the efficiency and accuracy of the proposed method.