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.

A multigrid method is proposed to compute the ground state solution of Bose-Einstein condensations by the finite element method based on the multilevel correction for eigenvalue problems and the multigrid method for linear boundary value problems. In this scheme, obtaining the optimal approximation for the ground state solution of Bose-Einstein condensates includes a sequence of solutions of the linear boundary value problems by the multigrid method on the multilevel meshes and some solutions of nonlinear eigenvalue problems some very low dimensional finite element space. The total computational work of this scheme can reach almost the same optimal order as solving the corresponding linear boundary value problem. Therefore, this type of multigrid scheme can improve the overall efficiency for the simulation of Bose-Einstein condensations. Some numerical experiments are provided to validate the efficiency of the proposed method.

We present results of simulations of the energetics and dynamics involved in the realization of the NV (nitrogen-vacancy) center in diamond. We use the self-consistent charge-density functional tight-binding approximation and show that when the nitrogen resides on a single substitutional site, it fails to attract a vacancy, hence no NV center can be formed. However, if it occupies a split interstitial site and two vacancies reside on the second or third neighbor sites, an NV center will form following annealing at temperatures as low as 300°C and 650°C, respectively. These results provide guidelines to experimentalists on how to increase the efficiency of NV formation in diamond.

A front tracking method combined with the real ghost fluid method (RGFM) is proposed for simulations of fluid interfaces in two-dimensional compressible flows. In this paper the Riemann problem is constructed along the normal direction of interface and the corresponding Riemann solutions are used to track fluid interfaces. The interface boundary conditions are defined by the RGFM, and the fluid interfaces are explicitly tracked by several connected marker points. The Riemann solutions are also used directly to update the flow states on both sides of the interface in the RGFM. In order to validate the accuracy and capacity of the new method, extensive numerical tests including the bubble advection, the Sod tube, the shock-bubble interaction, the Richtmyer-Meshkov instability and the gas-water interface, are simulated by using the Euler equations. The computational results are also compared with earlier computational studies and it shows good agreements including the compressible gas-water system with large density differences.

The first-order cross correlation and corresponding applications in the passive imaging are deeply studied by Garnier and Papanicolaou in their pioneer works. In this paper, the results of the first-order cross correlation are generalized to the second-order cross correlation. The second-order cross correlation is proven to be a statistically stable quantity, with respective to the random ambient noise sources. Specially, with proper time scales, the stochastic fluctuation for the second-order cross correlation converges much faster than the first-order one. Indeed, the convergent rate is of order , with 0 < α < 1. Besides, by using the stationary phase method in both homogeneous and scattering medium, similar behaviors of the singular components for the second-order cross correlation are obtained. Finally, two imaging methods are proposed to search for a target point reflector: One method is based on the imaging function, and has a better signal-to-noise rate; Another method is based on the geometric property, and can improve the bad range resolution of the imaging results.

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 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.

In this paper we consider PDE-constrained optimization problems which incorporate an H1 regularization control term. We focus on a time-dependent PDE, and consider both distributed and boundary control. The problems we consider include bound constraints on the state, and we use a Moreau-Yosida penalty function to handle this. We propose Krylov solvers and Schur complement preconditioning strategies for the different problems and illustrate their performance with numerical examples.

This paper concerns numerical computation of a fourth order eigenvalue problem. We first show the well-posedness of the source problem. An interior penalty discontinuous Galerkin method (C0IPG) using Lagrange elements is proposed and its convergence is studied. The method is then used to compute the eigenvalues. We show that the method is spectrally correct and prove the optimal convergence. Numerical examples are presented to validate the theory.

In the late stage of the mitotic cycle of eukaryotic cells, cytokinesis ensues during which a parent cell replicates its nucleus with the necessary genetical substances (i.e., DNAs and chromosomes) and splits into two similar offspring cells. This mitotic process involves complex chemical, biophysical andmechanical processes whose details are just beginning to be unfolded experimentally. In this paper, we propose a full 3-D hydrodynamical model using a phase field approach to study the cellular morphological change during cytokinesis. In this model, the force along the contracting ring induced by remodeling of actin-myosin filament on cell cortex layer at the division plane of the parent cell during cytokinesis, is approximated using a proxy force anchored on the newly formed nuclei. The symmetric or asymmetric cell division is simulated numerically with the model. Our numerical results show that the location of the division plane and the contracting force along the cytokinetic ring on the division plane are essential for the cell division. In addition, our numerical study also shows that, during cytokinesis, surface tension of the cell membrane also contributes to this process by retaining the morphological integrity of the offspring cells. This model and the accompanying numerical simulation tool provide a solid framework to build upon with more sophisticated whole cell models to probe the cell mitotic process.

We extend the Chebyshev-Legendre spectral method to multi-domain case for solving the two-dimensional vorticity equations. The schemes are formulated in Legendre-Galerkin method while the nonlinear term is collocated at Chebyshev-Gauss collocation points. We introduce proper basis functions in order that the matrix of algebraic system is sparse. The algorithm can be implemented efficiently and in parallel way. The numerical analysis results in the case of one-dimensional multi-domain are generalized to two-dimensional case. The stability and convergence of the method are proved. Numerical results are given.

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.

In this paper, an approach combining the DG method in space with CG method in time (CG-DG method) is developed to solve time-dependent Maxwell's equations when meta-materials are involved. Both the unconditional L2-stability and error estimate of order are obtained when polynomials of degree at most r is used for the temporal discretization and at most k for the spatial discretization. Numerical results in 3D are given to validate the theoretical results.

Because of stability constraints, most numerical schemes applied to hyperbolic systems of equations turn out to be costly when the flux term is multiplied by some very large scalar. This problem emerges with the M1 system of equations in the field of radiotherapy when considering heterogeneous media with very disparate densities. Additionally, the flux term of the M1 system is non-linear, and in order for the model to be well-posed the numerical solution needs to fulfill conditions called realizability. In this paper, we propose a numerical method that overcomes the stability constraint and preserves the realizability property. For this purpose, we relax the M1 system to obtain a linear flux term. Then we extend the stencil of the difference quotient to obtain stability. The scheme is applied to a radiotherapy dose calculation example.

In the paper, we develop and analyze a new mass-preserving splitting domain decomposition method over multiple sub-domains for solving parabolic equations. The domain is divided into non-overlapping multi-bock sub-domains. On the interfaces of sub-domains, the interface fluxes are computed by the semi-implicit (explicit) flux scheme. The solutions and fluxes in the interiors of sub-domains are computed by the splitting one-dimensional implicit solution-flux coupled scheme. The important feature is that the proposed scheme is mass conservative over multiple non-overlapping sub-domains. Analyzing the mass-preserving S-DDM scheme is difficult over non-overlapping multi-block sub-domains due to the combination of the splitting technique and the domain decomposition at each time step. We prove theoretically that our scheme satisfies conservation of mass over multi-block non-overlapping sub-domains and it is unconditionally stable. We further prove the convergence and obtain the error estimate in L2-norm. Numerical experiments confirm theoretical results.

We apply the immersed boundary (or IB) method to simulate deformation and detachment of a periodic array of wall-bounded biofilm colonies in response to a linear shear flow. The biofilm material is represented as a network of Hookean springs that are placed along the edges of a triangulation of the biofilm region. The interfacial shear stress, lift and drag forces acting on the biofilm colony are computed by using fluid stress jump method developed by Williams, Fauci and Gaver [Disc. Con-tin. Dyn. Sys. B 11(2):519–540, 2009], with a modified version of their exclusion filter. Our detachment criterion is based on the novel concept of an averaged equivalent continuum stress tensor defined at each IB point in the biofilm which is then used to determine a corresponding von Mises yield stress; wherever this yield stress exceeds a given critical threshold the connections to that node are severed, thereby signalling the onset of a detachment event. In order to capture the deformation and detachment behaviour of a biofilm colony at different stages of growth, we consider a family of four biofilm shapes with varying aspect ratio. For each aspect ratio, we varied the spacing between colonies to investigate role of spatial clustering in offering protection against detachment. Our numerical simulations focus on the behaviour of weak biofilms (with relatively low yield stress threshold) and investigate features of the fluid-structure interaction such as locations of maximum shear and increased drag. The most important conclusions of this work are: (a) reducing the spacing between colonies reduces drag by from 50 to 100% and alters the interfacial shear stress profile, suggesting that even weak biofilms may be able to grow into tall structures because of the protection they gain from spatial proximity with other colonies; (b) the commonly employed detachment strategy in biofilm models based only on interfacial shear stress can lead to incorrect or inaccurate results when applied to the study of shear induced detachment of weak biofilms. Our detachment strategy based on equivalent continuum stresses provides a unified and consistent IB framework that handles both sloughing and erosion modes of biofilm detachment, and is consistent with strategies employed in many other continuum based biofilm models.

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 paper, we propose an uniformly convergent adaptive finite element method with hybrid basis (AFEM-HB) for the discretization of singularly perturbed nonlinear eigenvalue problems under constraints with applications in Bose-Einstein condensation (BEC) and quantum chemistry. We begin with the time-independent Gross-Pitaevskii equation and show how to reformulate it into a singularly perturbed nonlinear eigenvalue problem under a constraint. Matched asymptotic approximations for the problem are reviewed to confirm the asymptotic behaviors of the solutions in the boundary/interior layer regions. By using the normalized gradient flow, we propose an adaptive finite element with hybrid basis to solve the singularly perturbed nonlinear eigenvalue problem. Our basis functions and the mesh are chosen adaptively to the small parameter ε. Extensive numerical results are reported to show the uniform convergence property of our method. We also apply the AFEM-HB to compute the ground and excited states of BEC with box/harmonic/optical lattice potential in the semiclassical regime (0 <ε≪C 1). In addition, we give a detailed error analysis of our AFEM-HB to a simpler singularly perturbed two point boundary value problem, show that our method has a minimum uniform convergence order

The purpose of this paper is to numerically realize the inverse scattering scheme proposed in [19] of reconstructing complex elastic objects by a single far-field measurement. The unknown elastic scatterers might consist of both rigid bodies and traction-free cavities with components of multiscale sizes presented simultaneously. We conduct extensive numerical experiments to show the effectiveness and efficiency of the imaging scheme proposed in [19]. Moreover, we develop a two-stage technique, which can significantly speed up the reconstruction to yield a fast imaging scheme.

We devise an efficient algorithm for the symbolic calculation of irreducible angular momentum and spin (LS) eigenspaces within the n-fold antisymmetrized tensor product ^n Vu, where n is the number of electrons and u = s,p,d,… denotes the atomic subshell. This is an essential step for dimension reduction in configuration-interaction (CI) methods applied to atomic many-electron quantum systems. The algorithm relies on the observation that each Lz eigenstate with maximal eigenvalue is also an L2 eigenstate (equivalently for Sz and S2), as well as the traversal of LS eigenstates using the lowering operators L_ and S_. Iterative application to the remaining states in ^nVu leads to an implicit simultaneous diagonalization. A detailed complexity analysis for fixed n and increasing subshell number u yields run time O(u3n–2). A symbolic computer algebra implementation is available online.

A finite difference method which is second-order accurate in time and in space is proposed for two-dimensional fractional percolation equations. Using the Fourier transform, a general approximation for the mixed fractional derivatives is analyzed. An approach based on the classical Crank-Nicolson scheme combined with the Richardson extrapolation is used to obtain temporally and spatially second-order accurate numerical estimates. Consistency, stability and convergence of the method are established. Numerical experiments illustrating the effectiveness of the theoretical analysis are provided.