Efficient algorithms for the simulation of strained heteroepitaxial growth with intermixing in 2+1 dimensions are presented. The first of these algorithms is an extension of the energy localization method [T. P. Schulze and P. Smereka, An energy localization principle and its application to fast kinetic Monte Carlo simulation of heteroepitaxial growth, J. Mech. Phys. Sol., 3 (2009), 521–538] from 1+1 to 2+1 dimensions. Two approximations of this basic algorithm are then introduced, one of which treats adatoms in a more efficient manner, while the other makes use of an approximation of the change in elastic energy in terms of local elastic energy density. In both cases, it is demonstrated that a reasonable level of fidelity is achieved. Results are presented showing how the film morphology is affected by misfit and deposition rate. In addition, simulations of stacked quantum dots are also presented.

The equilibrium metric for minimizing a continuous congested traffic model is the solution of a variational problem involving geodesic distances. The continuous equilibrium metric and its associated variational problem are closely related to the classical discrete Wardrop's equilibrium. We propose an adjoint state method to numerically approximate continuous traffic congestion equilibria through the continuous formulation. The method formally derives an adjoint state equation to compute the gradient descent direction so as to minimize a nonlinear functional involving the equilibrium metric and the resulting geodesic distances. The geodesic distance needed for the state equation is computed by solving a factored eikonal equation, and the adjoint state equation is solved by a fast sweeping method. Numerical examples demonstrate that the proposed adjoint state method produces desired equilibrium metrics and outperforms the subgradient marching method for computing such equilibrium metrics.

We propose an a-posteriori error/smoothness indicator for standard semi-discrete finite volume schemes for systems of conservation laws, based on the numerical production of entropy. This idea extends previous work by the first author limited to central finite volume schemes on staggered grids. We prove that the indicator converges to zero with the same rate of the error of the underlying numerical scheme on smooth flows under grid refinement. We construct and test an adaptive scheme for systems of equations in which the mesh is driven by the entropy indicator. The adaptive scheme uses a single nonuniform grid with a variable timestep. We show how to implement a second order scheme on such a space-time non uniform grid, preserving accuracy and conservation properties. We also give an example of a p-adaptive strategy.

In this paper the numerical solution of the two-dimensional sine-Gordon equation is studied. Split local artificial boundary conditions are obtained by the operator splitting method. Then the original problem is reduced to an initial boundary value problem on a bounded computational domain, which can be solved by the finite difference method. Several numerical examples are provided to demonstrate the effectiveness and accuracy of the proposed method, and some interesting propagation and collision behaviors of the solitary wave solutions are observed.

The present work is concerned with the derivation of numerical methods to approximate the radiation dose in external beam radiotherapy. To address this issue, we consider a moment approximation of radiative transfer, closed by an entropy minimization principle. The model under consideration is governed by a system of hyperbolic equations in conservation form supplemented by source terms. The main difficulty coming from the numerical approximation of this system is an explicit space dependence in the flux function. Indeed, this dependence will be seen to be stiff and specific numerical strategies must be derived in order to obtain the needed accuracy. A first approach is developed considering the 1D case, where a judicious change of variables allows to eliminate the space dependence in the flux function. This is not possible in multi-D. We therefore reinterpret the 1D scheme as a scheme on two meshes, and generalize this to 2D by alternating transformations between separate meshes. We call this procedure projection method. Several numerical experiments, coming from medical physics, illustrate the potential applicability of the developed method.

Two fundamental facts of the modern wave turbulence theory are 1) existence of power energy spectra in k-space, and 2) existence of "gaps" in this spectra corresponding to the resonance clustering. Accordingly, three wave turbulent regimes are singled out: kinetic, described by wave kinetic equations and power energy spectra;discrete, characterized by resonance clustering; and mesoscopic, where both types of wave field time evolution coexist. In this review paper we present the results on integrable dynamics of resonance clusters appearing in discrete and mesoscopic wave turbulent regimes. Using a novel method based on the notion of dynamical invariant we show that some of the frequently met clusters are integrable in quadratures for arbitrary initial conditions and some others-only for particular initial conditions. We also identify chaotic behaviour in some cases. Physical implications of the results obtained are discussed.

The probabilistic solutions of the nonlinear stochastic dynamic (NSD) systems with polynomial type of nonlinearity are investigated with the subspace-EPC method. The space of the state variables of large-scale nonlinear stochastic dynamic system excited by white noises is separated into two subspaces. Both sides of the Fokker-Planck-Kolmogorov (FPK) equation corresponding to the NSD system is then integrated over one of the subspaces. The FPK equation for the joint probability density function of the state variables in another subspace is formulated. Therefore, the FPK equation in low dimensions is obtained from the original FPK equation in high dimensions and it makes the problem of obtaining the probabilistic solutions of large-scale NSD systems solvable with the exponential polynomial closure method. Examples about the NSD systems with polynomial type of nonlinearity are given to show the effectiveness of the subspace-EPC method in these cases.

In this paper, we develop a formulation for solving equations containing higher spatial derivative terms in a spectral volume (SV) context; more specifically the emphasis is on handling equations containing third derivative terms. This formulation is based on the LDG (Local Discontinuous Galerkin) flux discretization method, originally employed for viscous equations containing second derivatives. A linear Fourier analysis was performed to study the dispersion and the dissipation properties of the new formulation. The Fourier analysis was utilized for two purposes: firstly to eliminate all the unstable SV partitions, secondly to obtain the optimal SV partition. Numerical experiments are performed to illustrate the capability of this formulation. Since this formulation is extremely local, it can be easily parallelized and a h-p adaptation is relatively straightforward to implement. In general, the numerical results are very promising and indicate that the approach has a great potential for higher dimension Korteweg-de Vries (KdV) type problems.

We propose a hierarchy of novel absorbing boundary conditions for the one-dimensional stationary Schrödinger equation with general (linear and nonlinear) potential. The accuracy of the new absorbing boundary conditions is investigated numerically for the computation of energies and ground-states for linear and nonlinear Schrödinger equations. It turns out that these absorbing boundary conditions and their variants lead to a higher accuracy than the usual Dirichlet boundary condition. Finally, we give the extension of these ABCs to N-dimensional stationary Schrödinger equations.

We propose a new multiscale method that couples molecular dynamics simulations (MD) at the atomic scale and finite element simulations (FE) at the continuum regime. By constructing the mass matrix and stiffness matrix dependent on coarsening of grids, we find a general form of the equations of motion for the atomic and continuum regions. In order to improve the simulation at finite temperatures, we propose a low-pass phonon filter near the interface between the atomic and continuum regions, which is transparent for low frequency phonons, but dampens the high frequency phonons.

Cavities and fractures significantly affect the flow paths in carbonate reservoirs and should be accurately accounted for in numerical models. Herein, we consider the problem of computing the effective permeability of rock samples based on high-resolution 3D CT scans containing millions of voxels. We use the Stokes-Brinkman equations in the entire domain, covering regions of free flow governed by the Stokes equations, porous Darcy flow, and transitions between them. The presence of different length scales and large (ten orders of magnitude) contrasts in permeability leads to highly ill-conditioned linear systems of equations, which are difficult to solve. To obtain a problem that is computationally tractable, we first analyze the relative importance of the Stokes and Darcy terms for a set of idealized 2D models. We find that, in terms of effective permeability, the Stokes-Brinkman equations are only applicable for a special parameter set where the effective free-flow permeability is less than four orders of magnitude different from the matrix permeability. All other cases can be accurately modeled with either the Stokes or the Darcy end-member flows, depending on if there do or do not exist percolating free-flow regions. The insights obtained are used to perform a direct computation of the effective permeability of a rock sample model with more than 8 million cells.

In this paper, a novel implementation of immersed interface method combined with Stokes solver on a MAC staggered grid for solving the steady two-fluid Stokes equations with interfaces. The velocity components along the interface are introduced as two augmented variables and the resulting augmented equation is then solved by the GMRES method. The augmented variables and/or the forces are related to the jumps in pressure and the jumps in the derivatives of both pressure and velocity, and are interpolated using cubic splines and are then applied to the fluid through the jump conditions. The Stokes equations are discretized on a staggered Cartesian grid via a second order finite difference method and solved by the conjugate gradient Uzawa-type method. The numerical results show that the overall scheme is second order accuracy. The major advantages of the present IIM-Stokes solver are the efficiency and flexibility in terms of types of fluid flow and different boundary conditions. The proposed method avoids solution of the pressure Poisson equation, and comparisons are made to show the advantages of time savings by the present method. The generalized two-phase Stokes solver with correction terms has also been applied to incompressible two-phase Navier-Stokes flow.