In this paper, we study a lattice Boltzmann method for the advection-diffusion equation with Neumann boundary conditions on general boundaries. A novel mass conservative scheme is introduced for implementing such boundary conditions, and is analyzed both theoretically and numerically.

Second order convergence is predicted by the theoretical analysis, and numerical investigations show that the convergence is at or close to the predicted rate. The numerical investigations include time-dependent problems and a steady-state diffusion problem for computation of effective diffusion coefficients.

An existing phase-fieldmodel of two immiscible fluids with a single soluble surfactant present is discussed in detail. We analyze the well-posedness of the model and provide strong evidence that it is mathematically ill-posed for a large set of physically relevant parameters. As a consequence, critical modifications to the model are suggested that substantially increase the domain of validity. Carefully designed numerical simulations offer informative demonstrations as to the sharpness of our theoretical results and the qualities of the physical model. A fully coupled hydrodynamic test-case demonstrates the potential to capture also non-trivial effects on the overall flow.

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.

We propose an all regime Lagrange-Projection like numerical scheme for the gas dynamics equations. By all regime, we mean that the numerical scheme is able to compute accurate approximate solutions with an under-resolved discretization with respect to the Mach number M, i.e. such that the ratio between the Mach number M and the mesh size or the time step is small with respect to 1. The key idea is to decouple acoustic and transport phenomenon and then alter the numerical flux in the acoustic approximation to obtain a uniform truncation error in term of M. This modified scheme is conservative and endowed with good stability properties with respect to the positivity of the density and the internal energy. A discrete entropy inequality under a condition on the modification is obtained thanks to a reinterpretation of the modified scheme in the Harten Lax and van Leer formalism. A natural extension to multi-dimensional problems discretized over unstructured mesh is proposed. Then a simple and efficient semi implicit scheme is also proposed. The resulting scheme is stable under a CFL condition driven by the (slow) material waves and not by the (fast) acoustic waves and so verifies the all regime property. Numerical evidences are proposed and show the ability of the scheme to deal with tests where the flow regime may vary from low to high Mach values.

Here we report a web server, the DelPhi web server, which utilizes DelPhi program to calculate electrostatic energies and the corresponding electrostatic potential and ionic distributions, and dielectric map. The server provides extra services to fix structural defects, as missing atoms in the structural file and allows for generation of missing hydrogen atoms. The hydrogen placement and the corresponding DelPhi calculations can be done with user selected force field parameters being either Charmm22, Amber98 or OPLS. Upon completion of the calculations, the user is given option to download fixed and protonated structural file, together with the parameter and Delphi output files for further analysis. Utilizing Jmol viewer, the user can see the corresponding structural file, to manipulate it and to change the presentation. In addition, if the potential map is requested to be calculated, the potential can be mapped onto the molecule surface. The DelPhi web server is available from http://compbio.clemson.edu/delphi_webserver.

In this paper, we propose a new conservative semi-Lagrangian (SL) finite difference (FD) WENO scheme for linear advection equations, which can serve as a base scheme for the Vlasov equation by Strang splitting [4]. The reconstruction procedure in the proposed SL FD scheme is the same as the one used in the SL finite volume (FV) WENO scheme [3]. However, instead of inputting cell averages and approximate the integral form of the equation in a FV scheme, we input point values and approximate the differential form of equation in a FD spirit, yet retaining very high order (fifth order in our experiment) spatial accuracy. The advantage of using point values, rather than cell averages, is to avoid the second order spatial error, due to the shearing in velocity (v) and electrical field (E) over a cell when performing the Strang splitting to the Vlasov equation. As a result, the proposed scheme has very high spatial accuracy, compared with second order spatial accuracy for Strang split SL FV scheme for solving the Vlasov-Poisson (VP) system. We perform numerical experiments on linear advection, rigid body rotation problem; and on the Landau damping and two-stream instabilities by solving the VP system. For comparison, we also apply (1) the conservative SL FD WENO scheme, proposed in [22] for incompressible advection problem, (2) the conservative SL FD WENO scheme proposed in [21] and (3) the non-conservative version of the SL FD WENO scheme in [3] to the same test problems. The performances of different schemes are compared by the error table, solution resolution of sharp interface, and by tracking the conservation of physical norms, energies and entropies, which should be physically preserved.

This paper studies a local discontinuous Galerkin method combined with fourth order exponential time differencing Runge-Kutta time discretization and a fourth order conservative method for solving the nonlinear Schrödinger equations. Based on different choices of numerical fluxes, we propose both energy-conserving and energy-dissipative local discontinuous Galerkin methods, and have proven the error estimates for the semi-discrete methods applied to linear Schrödinger equation. The numerical methods are proven to be highly efficient and stable for long-range soliton computations. Extensive numerical examples are provided to illustrate the accuracy, efficiency and reliability of the proposed methods.

A recent work of Li et al. [Numer. Math. Theor. Meth. Appl., 1(2008), pp. 92-112] proposed a finite volume solver to solve 2D steady Euler equations. Although the Venkatakrishnan limiter is used to prevent the non-physical oscillations nearby the shock region, the overshoot or undershoot phenomenon can still be observed. Moreover, the numerical accuracy is degraded by using Venkatakrishnan limiter. To fix the problems, in this paper the WENO type reconstruction is employed to gain both the accurate approximations in smooth region and non-oscillatory sharp profiles near the shock discontinuity. The numerical experiments will demonstrate the efficiency and robustness of the proposed numerical strategy.

The accurate simulation of disperse two-phase flows, where a discrete particulate condensed phase is transported by a carrier gas, is crucial for many applications; Eulerian approaches are well suited for high performance computations of such flows. However when the particles from the disperse phase have a significant inertia compared to the time scales of the flow, particle trajectory crossing (PTC) occurs i.e. the particle velocity distribution at a given location can become multi-valued. To properly account for such a phenomenon many Eulerian moment methods have been recently proposed in the literature. The resulting models hardly comply with a full set of desired criteria involving: 1- ability to reproduce the physics of PTC, at least for a given range of particle inertia, 2- well-posedness of the resulting set of PDEs on the chosen moments as well as guaranteed realizability, 3- capability of the model to be associated with a high order realizable numerical scheme for the accurate resolution of particle segregation in turbulent flows. The purpose of the present contribution is to introduce a multi-variate Anisotropic Gaussian closure for such particulate flows, in the spirit of the closure that has been suggested for out-of-equilibrium gas dynamics and which satisfies the three criteria. The novelty of the contribution is three-fold. First we derive the related moment system of conservation laws with source terms, and justify the use of such a model in the context of high Knudsen numbers, where collision operators play no role. We exhibit the main features and advantages in terms of mathematical structure and realizability. Then a second order accurate and realizable MUSCL/HLL scheme is proposed and validated. Finally the behavior of the method for the description of PTC is thoroughly investigated and its ability to account accurately for inertial particulate flow dynamics in typical configurations is assessed.

A cluster dynamics model based on rate theory has been developed to describe the accumulation and diffusion processes of helium in tungsten under helium implantation alone or synergistic irradiation with neutron, by involving different types of objects, adopting up-to-date parameters and complex reaction processes as well as considering the diffusion process along with depth. The calculated results under different conditions are in good agreement with experiments much well. The model describes the behavior of helium in tungsten within 2D space of defect type/size and depth on different ions incident conditions (energies and fluences) and material conditions (system temperature and existent sinks), by including the synergistic effect of helium-neutron irradiations and the influence of inherent sinks (dislocation lines and grain boundaries). The model, coded as IRadMat, would be universally applicable to the evolution of defects for ions/neutron irradiated on plasma-facing materials.

In this paper, we present some efficient numerical schemes to solve a two-phase hydrodynamics coupled phase field model with moving contact line boundary conditions. The model is a nonlinear coupling system, which consists the Navier-Stokes equations with the general Navier Boundary conditions or degenerated Navier Boundary conditions, and the Allen-Cahn type phase field equations with dynamical contact line boundary condition or static contact line boundary condition. The proposed schemes are linear and unconditionally energy stable, where the energy stabilities are proved rigorously. Various numerical tests are performed to show the accuracy and efficiency thereafter.

High order discretization schemes play more important role in fractional operators than classical ones. This is because usually for classical derivatives the stencil for high order discretization schemes is wider than low order ones; but for fractional operators the stencils for high order schemes and low order ones are the same. Then using high order schemes to solve fractional equations leads to almost the same computational cost with first order schemes but the accuracy is greatly improved. Using the fractional linear multistep methods, Lubich obtains the v-th order (v < 6) approximations of the α-th derivative (α > 0) or integral (α < 0) [Lubich, SIAM J. Math. Anal., 17, 704-719, 1986], because of the stability issue the obtained scheme can not be directly applied to the space fractional operator with α Є (1,2) for time dependent problem. By weighting and shifting Lubich’s 2nd order discretization scheme, in [Chen & Deng, SINUM, arXiv:1304.7425] we derive a series of effective high order discretizations for space fractional derivative, called WSLD operators there. As the sequel of the previous work, we further provide new high order schemes for space fractional derivatives by weighting and shifting Lubich’s 3rd and 4th order discretizations. In particular, we prove that the obtained 4th order approximations are effective for space fractional derivatives. And the corresponding schemes are used to solve the space fractional diffusion equation with variable coefficients.

In this paper, preconditioned iterative methods for solving two-dimensional space-fractional diffusion equations are considered. The fractional diffusion equation is discretized by a second-order finite difference scheme, namely, the Crank-Nicolson weighted and shifted Grünwald difference (CN-WSGD) scheme proposed in [W. Tian, H. Zhou and W. Deng, A class of second order difference approximation for solving space fractional diffusion equations, Math. Comp., 84 (2015) 1703-1727]. For the discretized linear systems, we first propose preconditioned iterative methods to solve them. Then we apply the D’Yakonov ADI scheme to split the linear systems and solve the obtained splitting systems by iterative methods. Two preconditioned iterative methods, the preconditioned generalized minimal residual (preconditioned GMRES) method and the preconditioned conjugate gradient normal residual (preconditioned CGNR) method, are proposed to solve relevant linear systems. By fully exploiting the structure of the coefficient matrix, we design two special kinds of preconditioners, which are easily constructed and are able to accelerate convergence of iterative solvers. Numerical results show the efficiency of our preconditioners.

We have developed efficient numerical algorithms for solving 3D steady-state Poisson-Nernst-Planck (PNP) equations with excess chemical potentials described by the classical density functional theory (cDFT). The coupled PNP equations are discretized by a finite difference scheme and solved iteratively using the Gummel method with relaxation. The Nernst-Planck equations are transformed into Laplace equations through the Slotboom transformation. Then, the algebraic multigrid method is applied to efficiently solve the Poisson equation and the transformed Nernst-Planck equations. A novel strategy for calculating excess chemical potentials through fast Fourier transforms is proposed, which reduces computational complexity from O(N2) to O(NlogN), where N is the number of grid points. Integrals involving the Dirac delta function are evaluated directly by coordinate transformation, which yields more accurate results compared to applying numerical quadrature to an approximated delta function. Numerical results for ion and electron transport in solid electrolyte for lithiumion (Li-ion) batteries are shown to be in good agreement with the experimental data and the results from previous studies.

Various conceptual models exist for numerical simulation of fluid flow in fractured porous media, such as dual-porosity model and equivalent continuum model. As a promising model, the discrete-fracture model has been received more attention in the past decade. It can be used both as a stand-alone tool as well as for the evaluation of effective parameters for the continuum models. Various numerical methods have been applied to the discrete-fracture model, including control volume finite difference, Galerkin and mixed finite element methods. All these methods have inherent limitations in accuracy and applicabilities. In this work, we developed a new numerical scheme for the discrete-fracture model by using mimetic finite difference method. The proposed numerical model is applicable in arbitrary unstructured gridcells with full-tensor permeabilities. The matrix-fracture and fracture-fracture fluxes are calculated based on powerful features of the mimetic finite difference method, while the upstream finite volume scheme is used for the approximation of the saturation equation. Several numerical tests in 2D and 3D are carried out to demonstrate the efficiency and robustness of the proposed numerical model.

The definition of a molecular surface which is physically sound and computationally efficient is a very interesting and long standing problem in the implicit solvent continuum modeling of biomolecular systems as well as in the molecular graphics field. In this work, two molecular surfaces are evaluated with respect to their suitability for electrostatic computation as alternatives to the widely used Connolly-Richards surface: the blobby surface, an implicit Gaussian atom centered surface, and the skin surface. As figures of merit, we considered surface differentiability and surface area continuity with respect to atom positions, and the agreement with explicit solvent simulations. Geometric analysis seems to privilege the skin to the blobby surface, and points to an unexpected relationship between the non connectedness of the surface, caused by interstices in the solute volume, and the surface area dependence on atomic centers. In order to assess the ability to reproduce explicit solvent results, specific software tools have been developed to enable the use of the skin surface in Poisson-Boltzmann calculations with the DelPhi solver. The results indicate that the skin and Connolly surfaces have a comparable performance from this last point of view.

We study the settling of solid particles in a viscous incompressible fluid contained within a two-dimensional channel, where the mass density of the particles is greater than that of the fluid. The fluid-structure interaction problem is simulated numerically using the immersed boundary method, where the added mass is incorporated using a Boussinesq approximation. Simulations are performed with a single circular particle, and also with two particles in various initial configurations. The terminal particle settling velocity and drag coefficient correspond closely with other theoretical, experimental and numerical results, and the particle trajectories reproduce the expected behavior qualitatively. In particular, simulations of a pair of interacting particles similar drafting-kissing-tumbling dynamics to that observed in other experimental and numerical studies.

We consider the design of an effective and reliable adaptive finite element method (AFEM) for the nonlinear Poisson-Boltzmann equation (PBE). We first examine the two-term regularization technique for the continuous problem recently proposed by Chen, Holst and Xu based on the removal of the singular electrostatic potential inside biomolecules; this technique made possible the development of the first complete solution and approximation theory for the Poisson-Boltzmann equation, the first provably convergent discretization and also allowed for the development of a provably convergent AFEM. However, in practical implementation, this two-term regularization exhibits numerical instability. Therefore, we examine a variation of this regularization technique which can be shown to be less susceptible to such instability. We establish a priori estimates and other basic results for the continuous regularized problem, as well as for Galerkin finite element approximations. We show that the new approach produces regularized continuous and discrete problems with the same mathematical advantages of the original regularization. We then design an AFEM scheme for the new regularized problem and show that the resulting AFEM scheme is accurate and reliable, by proving a contraction result for the error. This result, which is one of the first results of this type for nonlinear elliptic problems, is based on using continuous and discrete a prioriL∞ estimates. To provide a high-quality geometric model as input to the AFEM algorithm, we also describe a class of feature-preserving adaptive mesh generation algorithms designed specifically for constructing meshes of biomolecular structures, based on the intrinsic local structure tensor of the molecular surface. All of the algorithms described in the article are implemented in the Finite Element Toolkit (FETK), developed and maintained at UCSD. The stability advantages of the new regularization scheme are demonstrated with FETK through comparisons with the original regularization approach for a model problem. The convergence and accuracy of the overall AFEMalgorithmis also illustrated by numerical approximation of electrostatic solvation energy for an insulin protein.

We propose a general framework of computing interfacial structures between two modulated phases. Specifically we propose to use a computational box consisting of two half spaces, each occupied by a modulated phase with given position and orientation. The boundary conditions and basis functions are chosen to be commensurate with the bulk phases. We observe that the ordered nature of modulated structures stabilizes the interface, which enables us to obtain optimal interfacial structures by searching local minima of the free energy landscape. The framework is applied to the Landau-Brazovskii model to investigate interfaces between modulated phases with different relative positions and orientations. Several types of novel complex interfacial structures emerge from the calculations.