In this paper, we aim to solve one and two dimensional hyperbolic conservation laws on arbitrarily distributed point clouds. The initial condition is given on such a point cloud, and the algorithm solves for point values of the solution at later time also on this point cloud. By using the Voronoi technique and by introducing a grouping algorithm, we divide the computational domain into non-overlapping cells. Each cell is a polygon and contains a minimum number of the given points to ensure accuracy. We carefully select points in each cell during the grouping procedure, and hence are able to interpolate or fit the discrete initial values with piecewise polynomials. By adapting the traditional discontinuous Galerkin method on the constructed polygonal mesh, we obtain a stable, conservative and high order method. Numerical results for both one and two dimensional scalar equations and Euler systems of compressible gas dynamics are provided to illustrate the good behavior of our mesh generation algorithm as well as the numerical scheme.

We introduce a new adaptive method for analyzing nonlinear and nonstationary data. This method is inspired by the empirical mode decomposition (EMD) method and the recently developed compressed sensing theory. The main idea is to look for the sparsest representation of multiscale data within the largest possible dictionary consisting of intrinsic mode functions of the form {a(t) cos(θ(t))}, where a ≥ 0 is assumed to be smoother than cos(θ(t)) and θ is a piecewise smooth increasing function. We formulate this problem as a nonlinear L1 optimization problem. Further, we propose an iterative algorithm to solve this nonlinear optimization problem recursively. We also introduce an adaptive filter method to decompose data with noise. Numerical examples are given to demonstrate the robustness of our method and comparison is made with the EMD method. One advantage of performing such a decomposition is to preserve some intrinsic physical property of the signal, such as trend and instantaneous frequency. Our method shares many important properties of the original EMD method. Because our method is based on a solid mathematical formulation, its performance does not depend on numerical parameters such as the number of shifting or stop criterion, which seem to have a major effect on the original EMD method. Our method is also less sensitive to noise perturbation and the end effect compared with the original EMD method.

In this paper, we analyze implicit-explicit (IMEX) Runge-Kutta (RK) time discretization methods for solving linear convection-diffusion equations. The diffusion operator is treated implicitly via the embedded discontinuous Galerkin (EDG) method and the convection operator explicitly via the upwinding discontinuous Galerkin method.

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.

Local multiscale methods often construct multiscale basis functions in the offline stage without taking into account input parameters, such as source terms, boundary conditions, and so on. These basis functions are then used in the online stage with a specific input parameter to solve the global problem at a reduced computational cost. Recently, online approaches have been introduced, where multiscale basis functions are adaptively constructed in some regions to reduce the error significantly. In multiscale methods, it is desired to have only 12 iterations to reduce the error to a desired threshold. Using Generalized Multiscale Finite Element Framework [10], it was shown that by choosing sufficient number of offline basis functions, the error reduction can be made independent of physical parameters, such as scales and contrast. In this paper, our goal is to improve this. Using our recently proposed approach [4] and