In this paper, we introduce a high-order accurate constrained transport type finite volume method to solve ideal magnetohydrodynamic equations on two-dimensional triangular meshes. A new divergence-free WENO-based reconstruction method is developed to maintain exactly divergence-free evolution of the numerical magnetic field. In this formulation, the normal component of the magnetic field at each face of a triangle is reconstructed uniquely and with the desired order of accuracy. Additionally, a new weighted flux interpolation approach is also developed to compute the z-component of the electric field at vertices of grid cells. We also present numerical examples to demonstrate the accuracy and robustness of the proposed scheme.

This paper concerns the computation of nonlinear crest distributions for irregular Stokes waves, and a numerical algorithm based on the Fast Fourier Transform (FFT) technique has been developed for carrying out the nonlinear computations. In order to further improve the computational efficiency, a new Transformed Rayleigh procedure is first proposed as another alternative for computing the nonlinear wave crest height distributions, and the corresponding computer code has also been developed. In the proposed Transformed Rayleigh procedure, the transformation model is chosen to be a monotonic exponential function, calibrated such that the first three moments of the transformed model match the moments of the true process. The numerical algorithm based on the FFT technique and the proposed Transformed Rayleigh procedure have been applied to calculating the wave crest distributions of a sea state with a Bretschneider spectrum and a sea state with the surface elevation data measured at the Poseidon platform. It is demonstrated in these two cases that the numerical algorithm based on the FFT technique and the proposed Transformed Rayleigh procedure can offer better predictions than those from using the empirical wave crest distribution models. Meanwhile, it is found that our proposed Transformed Rayleigh procedure can compute nonlinear crest distributions more than 25 times faster than the numerical algorithm based on the FFT technique.

This paper introduces a two-stage model for multi-channel image segmentation, which is motivated by minimal surface theory. Indeed, in the first stage, we acquire a smooth solution u from a convex variational model related to minimal surface property and different data fidelity terms are considered. This minimization problem is solved efficiently by the classical primal-dual approach. In the second stage, we adopt thresholding to segment the smoothed image u. Here, instead of using K-means to determine the thresholds, we propose a more stable hill-climbing procedure to locate the peaks on the 3D histogram of u as thresholds, in the meantime, this algorithm can also detect the number of segments. Finally, numerical results demonstrate that the proposed method is very robust against noise and superior to other image segmentation approaches.

In this paper, we study the selectivity of the potassium channel KcsA by a recently developed image-charge solvation method (ICSM) combined with molecular dynamics simulations. The hybrid solvation model in the ICSM is able to demonstrate atomistically the function of the selectivity filter of the KcsA channel when potassium and sodium ions are considered and their distributions inside the filter are simulated. Our study also shows that the reaction field effect, explicitly accounted for through image charge approximation in the ICSM model, is necessary in reproducing the correct selectivity property of the potassium channels.

In this paper, we propose a new type of weighted essentially non-oscillatory (WENO) limiter, which belongs to the class of Hermite WENO (HWENO) limiters, for the Runge-Kutta discontinuous Galerkin (RKDG) methods solving hyperbolic conservation laws. This new HWENO limiter is a modification of the simple WENO limiter proposed recently by Zhong and Shu [29]. Both limiters use information of the DG solutions only from the target cell and its immediate neighboring cells, thus maintaining the original compactness of the DG scheme. The goal of both limiters is to obtain high order accuracy and non-oscillatory properties simultaneously. The main novelty of the new HWENO limiter in this paper is to reconstruct the polynomial on the target cell in a least square fashion [8] while the simple WENO limiter [29] is to use the entire polynomial of the original DG solutions in the neighboring cells with an addition of a constant for conservation. The modification in this paper improves the robustness in the computation of problems with strong shocks or contact discontinuities, without changing the compact stencil of the DG scheme. Numerical results for both one and two dimensional equations including Euler equations of compressible gas dynamics are provided to illustrate the viability of this modified limiter.

In this paper, we will present a high-order, well-conditioned boundary element method (BEM) based on Müller's hypersingular second kind integral equation formulation to accurately compute electrostatic potentials in the presence of inhomogeneity embedded within layered media. We consider two types of inhomogeneities: the first one is a simple model of an ion channel which consists of a finite height cylindrical cavity embedded in a layered electrolytes/membrane environment, and the second one is a Janus particle made of two different semi-spherical dielectric materials. Both types of inhomogeneities have relevant applications in biology and colloidal material, respectively. The proposed BEM gives $\mathcal{O}$(1) condition numbers, allowing fast convergence of iterative solvers compared to previous work using first kind of integral equations. We also show that the second order basis converges faster and is more accurate than the first order basis for the BEM.

The unified lattice Boltzmann model is extended to the quadtree grids for simulation of fluid flow through porous media. The unified lattice Boltzmann model is capable of simulating flow in porous media at various scales or in systems where multiple length scales coexist. The quadtree grid is able to provide a high-resolution approximation to complex geometries, with great flexibility to control local grid density. The combination of the unified lattice Boltzmann model and the quadtree grids results in an efficient numerical model for calculating permeability of multi-scale porous media. The model is used for permeability calculation for three systems, including a fractured system used in a previous study, a Voronoi tessellation system, and a computationally-generated pore structure of fractured shale. The results are compared with those obtained using the conventional lattice Boltzmann model or the unified lattice Boltzmann model on rectangular or uniform square grid. It is shown that the proposed model is an accurate and efficient tool for flow simulation in multi-scale porous media. In addition, for the fractured shale, the contribution of flow in matrix and fractures to the overall permeability of the fractured shale is studied systematically.

The purpose of this paper is to develop and test novel invariant-preserving finite difference schemes for both the Camassa-Holm (CH) equation and one of its 2-component generalizations (2CH). The considered PDEs are strongly nonlinear, admitting soliton-like peakon solutions which are characterized by a slope discontinuity at the peak in the wave shape, and therefore suitable for modeling both short wave breaking and long wave propagation phenomena. The proposed numerical schemes are shown to preserve two invariants, momentum and energy, hence numerically producing wave solutions with smaller phase error over a long time period than those generated by other conventional methods. We first apply the scheme to the CH equation and showcase the merits of considering such a scheme under a wide class of initial data. We then generalize this scheme to the 2CH equation and test this scheme under several types of initial data.

In this study long bubble rising in a narrow channel was investigated using multiphase lattice Boltzmann method. The problem is known as a Bretherton or Taylor bubble flow [2] and is used here to verify the performance of the scheme proposed by [13]. The scheme is modified by incorporation of multiple relaxation time (MRT) collision scheme according to the original suggestion of the author. The purpose is to improve the stability of the method. The numerical simulation results show a good agreement with analytic solution provided by [2]. Moreover, the convergence study demonstrates that the method achieves more than the first order of convergence. The paper also investigates the influence of simulation parameters on the interface resolution and shape.

We study pseudo-arclength continuation methods for both Rydberg-dressed Bose-Einstein condensates (BEC), and binary Rydberg-dressed BEC which are governed by the Gross-Pitaevskii equations (GPEs). A divide-and-conquer technique is proposed for rescaling the range/ranges of nonlocal nonlinear term/terms, which gives enough information for choosing a proper stepsize. This guarantees that the solution curve we wish to trace can be precisely approximated. In addition, the ground state solution would successfully evolve from one peak to vortices when the affect of the rotating term is imposed. Moreover, parameter variables with different number of components are exploited in curve-tracing. The proposed methods have the advantage of tracing the ground state solution curve once to compute the contours for various values of the coefficients of the nonlocal nonlinear term/terms. Our numerical results are consistent with those published in the literatures.

We study the numerical performance of a continuous data assimilation (downscaling) algorithm, based on ideas from feedback control theory, in the context of the two-dimensional incompressible Navier-Stokes equations. Our model problem is to recover an unknown reference solution, asymptotically in time, by using continuous-in-time coarse-mesh nodal-point observational measurements of the velocity field of this reference solution (subsampling), as might be measured by an array of weather vane anemometers. Our calculations show that the required nodal observation density is remarkably less than what is suggested by the analytical study; and is in fact comparable to the number of numerically determining Fourier modes, which was reported in an earlier computational study by the authors. Thus, this method is computationally efficient and performs far better than the analytical estimates suggest.