This paper presents a modified Loop’s subdivision algorithm for studying the deformation of a single capsule, the hydrodynamic interaction between two capsules and the hydrodynamic diffusion of a suspension of capsules in bounded shear flow. A subdivision thin-shell model is employed to compute the forces generated on the surface of the elastic capsule during deformation. The capsule surface is approximated using the modified Loop’s subdivision scheme which guarantees bounded curvature and C1 continuity everywhere on the limit surface. The present numerical technique has been validated by studying the deformation of a spherical capsule in shear flow. Computations are also performed for a biconcave capsule over a wide range of shear rates and viscosity ratios to investigate its dynamics. In addition, the hydrodynamic interaction between two elastic capsules in bounded shear flow is studied. Depending on the wall separation distance, the trajectory-bifurcation points that separate reversing and crossing motions for both spherical and biconcave capsules can be found. Compared to the spherical capsules, the biconcave capsules exhibit additional types of interaction such as rotation and head-on collision. The head-on collision results in a large trajectory shift which contribute to the hydrodynamic diffusion of a suspension. A suspension of a large number of biconcave capsules in shear flow is also simulated to show the ability of the modified scheme in running a large-scale simulation over a long period of time.

A Lagrangian surface hopping algorithm is implemented to study the two dimensional massless Dirac equation for Graphene with an electrostatic potential, in the semiclassical regime. In this problem, the crossing of the energy levels of the system at Dirac points requires a particular treatment in the algorithm in order to describe the quantum transition—characterized by the Landau-Zener probability— between different energy levels. We first derive the Landau-Zener probability for the underlying problem, then incorporate it into the surface hopping algorithm. We also show that different asymptotic models for this problem derived in [O. Morandi, F. Schurrer, J. Phys. A:Math. Theor. 44 (2011) 265301]may give different transition probabilities. We conduct numerical experiments to compare the solutions to the Dirac equation, the surface hopping algorithm, and the asymptotic models of [O. Morandi, F. Schurrer, J. Phys. A: Math. Theor. 44 (2011) 265301].

Volume-preserving algorithms (VPAs) for the charged particles dynamics is preferred because of their long-term accuracy and conservativeness for phase space volume. Lie algebra and the Baker-Campbell-Hausdorff (BCH) formula can be used as a fundamental theoretical tool to construct VPAs. Using the Lie algebra structure of vector fields, we split the volume-preserving vector field for charged particle dynamics into three volume-preserving parts (sub-algebras), and find the corresponding Lie subgroups. Proper combinations of these subgroups generate volume preserving, second order approximations of the original solution group, and thus second order VPAs. The developed VPAs also show their significant effectiveness in conserving phase-space volume exactly and bounding energy error over long-term simulations.

In this paper, we introduce and study a new method for solving inverse source problems, through a working model that arises in bioluminescence tomography (BLT). In the BLT problem, one constructs quantitatively the bioluminescence source distribution inside a small animal from optical signals detected on the animal's body surface. The BLT problem possesses strong ill-posedness and often the Tikhonov regularization is used to obtain stable approximate solutions. In conventional Tikhonov regularization, it is crucial to choose a proper regularization parameter for trade off between the accuracy and stability of approximate solutions. The new method is based on a combination of the boundary condition and the boundary measurement in a parameter-dependent single complex Robin boundary condition, followed by the Tikhonov regularization. By properly adjusting the parameter in the Robin boundary condition, we achieve two important properties for our new method: first, the regularized solutions are uniformly stable with respect to the regularization parameter so that the regularization parameter can be chosen based solely on the consideration of the solution accuracy; second, the convergence order of the regularized solutions reaches one with respect to the noise level. Then, the finite element method is used to compute numerical solutions and a new finite element error estimate is derived for discrete solutions. These results improve related results found in the existing literature. Several numerical examples are provided to illustrate the theoretical results.

In a two-dimensional (2D) photonic crystal (PhC) composed of circular cylinders (dielectric rods or air holes) on a square or triangular lattice, various PhC devices can be created by removing or modifying some cylinders. Most existing numerical methods for PhC devices give rise to large sparse or smaller but dense linear systems, all of which are expensive to solve if the device is large. In a previous work [Z. Hu et al., Optics Express, 16 (2008), 17383-17399], an efficient Dirichlet-to-Neumann (DtN) map method was developed for general 2D PhC devices with an infinite background PhC to take full advantage of the underlying lattice structure. The DtN map of a unit cell is an operator that maps the wave field to its normal derivative on the cell boundary and it allows one to avoid computing the wave field in the interior of the unit cell. In this paper, we extend the DtN map method to PhC devices with a finite background PhC. Since there is no bandgap effect to confine the light in a finite PhC, a different technique for truncating the domain is needed. We enclose the finite structure with a layer of empty boundary and corner unit cells, and approximate the DtN maps of these cells based on expanding the scattered wave in outgoing plane waves. Our method gives rise to a relatively small and sparse linear systems that are particularly easy to solve.

Neighbour search (NS) is the core of any implementations of smoothed particle hydrodynamics (SPH). In this paper,we present an efficient neighbour search method based on the plane sweep (PW) algorithm with N being the number of SPH particles. The resulting method, dubbed the PWNS method, is totally independent of grids (i.e., purely meshfree) and capable of treating variable smoothing length, arbitrary particle distribution and heterogenous kernels. Several state-of-the-art data structures and algorithms, e.g., the segment tree and the Morton code, are optimized and implemented. By simply allowingmultiple lines to sweep the SPH particles simultaneously from different initial positions, a parallelization of the PWNS method with satisfactory speedup and load-balancing can be easily achieved. That is, the PWNS SPH solver has a great potential for large scale fluid dynamics simulations.

An efficient and accurate numerical scheme is proposed for solving the transverse electric (TE) mode electromagnetic (EM) propagation problem in two-dimensional earth. The scheme is based on the alternating direction finite-difference time-domain (ADI-FDTD) method. Unlike the conventional upward continuation approach for the earth-air interface, an integral formulation for the interface boundary is developed and it is effectively incorporated to the ADI solver. Stability and convergence analysis together with an error estimate are presented. Numerical simulations are carried out to validate the proposed method, and the advantage of the present method over the popular Du-Fort-Frankel scheme is clearly demonstrated. Examples of the electromagnetic field propagation in the ground with anomaly further verify the effectiveness of the proposed scheme.

In this paper, a remapping-free adaptive GRP method for one dimensional (1-D) compressible flows is developed. Based on the framework of finite volume method, the 1-D Euler equations are discretized on moving volumes and the resulting numerical fluxes are computed directly by the GRP method. Thus the remapping process in the earlier adaptive GRP algorithm [17,18] is omitted. By adopting a flexible moving mesh strategy, this method could be applied for multi-fluid problems. The interface of two fluids will be kept at the node of computational grids and the GRP solver is extended at the material interfaces of multi-fluid flows accordingly. Some typical numerical tests show competitive performances of the new method, especially for contact discontinuities of one fluid cases and the material interface tracking of multi-fluid cases.

ArbiTER (Arbitrary Topology Equation Reader) is a new code for solving linear eigenvalue problems arising from a broad range of physics and geometry models. The primary application area envisioned is boundary plasma physics in magnetic confinement devices; however ArbiTER should be applicable to other science and engineering fields as well. The code permits a variable numbers of dimensions, making possible application to both fluid and kinetic models. The use of specialized equation and topology parsers permits a high degree of flexibility in specifying the physics and geometry.

We present a numerical method to solve the Vlasov-Poisson-Fokker-Planck (VPFP) system using the NRxx method proposed in [4, 7, 9]. A globally hyperbolic moment system similar to that in [23] is derived. In this system, the Fokker-Planck (FP) operator term is reduced into the linear combination of the moment coefficients, which can be solved analytically under proper truncation. The non-splitting method, which can keep mass conservation and the balance law of the total momentum, is used to solve the whole system. A numerical problem for the VPFP system with an analytic solution is presented to indicate the spectral convergence with the moment number and the linear convergence with the grid size. Two more numerical experiments are tested to demonstrate the stability and accuracy of the NRxx method when applied to the VPFP system.

A lattice Kinetic Monte Carlo (KMC) approach is considered to study the statistical properties of the diffusion of Pt atom clusters on a Pt(111) surface. The interatomic potential experienced by the diffusing atoms is calculated by the embedded atom method and the hopping barrier for the allowed atomic movements are calculated using the Nudged Elastic Band method. The diffusion coefficient is computed for various cluster sizes and system temperatures. The obtained results are in agreement with the ones obtained in previous experimental and theoretical works. A simple scaling argument is proposed for the size dependence of the diffusion coefficient’s pre-factor. A detailed statistical analysis of the event by event KMC dynamics reveals two important and co-existing mechanisms for the diffusion of the cluster’s center of mass. At low temperatures (below T = 400K) the dominating mechanism responsible for the displacement of the cluster’s center of mass is the periphery (or edge) diffusion of the atoms. At high temperatures (above T = 800K) the dissociation and recombination of the clusters becomes more and more important.

The numerical solution of blow-up problems for nonlinear wave equations on unbounded spatial domains is considered. Applying the unified approach, which is based on the operator splitting method, we construct the efficient nonlinear local absorbing boundary conditions for the nonlinear wave equation, and reduce the nonlinear problem on the unbounded spatial domain to an initial-boundary-value problem on a bounded domain. Then the finite difference method is used to solve the reduced problem on the bounded computational domain. Finally, a broad range of numerical examples are given to demonstrate the effectiveness and accuracy of our method, and some interesting propagation and behaviors of the blow-up problems for nonlinear wave equations are observed.

A new criterion is presented to detect global convergence to steady state, and to identify local transient characteristics, during rarefied gas flow simulations performed using the direct simulation Monte Carlo (DSMC) method. Unlike deterministic computational fluid dynamics (CFD) schemes, DSMC is generally subject to large statistical scatter in instantaneous flow property evaluations, which prevents the use of residual tracking procedures as are often employed in CFD simulations. However, reliable prediction of the time to reach steady state is necessary for initialization of DSMC sampling operations. Techniques currently used in DSMC to identify steady state convergence are usually insensitive to weak transient behavior in small regions of relatively low density or recirculating flow. The proposed convergence criterion is developed with the goal of properly identifying such weak transient behavior, while adding negligible computational expense and allowing simple implementation in any existing DSMC code. Benefits of the proposed technique over existing convergence detection methods are demonstrated for representative nozzle/plume expansion flow, hypersonic blunt body flow and driven cavity flow problems.

We introduce a new multigrid method to study the lattice statics model arising from nanoindentation. A constrained Cauchy-Born elasticity model is used as the coarse-grid operator. This method accelerates the relaxation process and considerably reduces the computational cost. In particular, it saves quite a bit when dislocations nucleate and move, as demonstrated by the simulation results.

A novel method for boundary constrained tetrahedral mesh generation is proposed based on Advancing Front Technique (AFT) and conforming Delaunay triangulation. Given a triangulated surface mesh, AFT is firstly applied to mesh several layers of elements adjacent to the boundary. The rest of the domain is then meshed by the conforming Delaunay triangulation. The non-conformal interface between two parts of meshes are adjusted. Mesh refinement and mesh optimization are then preformed to obtain a more reasonable-sized mesh with better quality. Robustness and quality of the proposed method is shown. Convergence proof of each stage as well as the whole algorithm is provided. Various numerical examples are included as well as the quality of the meshes.

We propose a numerical procedure to extend to full aperture the acoustic far-field pattern (FFP) when measured in only few observation angles. The reconstruction procedure is a multi-step technique that combines a total variation regularized iterative method with the standard Tikhonov regularized pseudo-inversion. The proposed approach distinguishes itself from existing solution methodologies by using an exact representation of the total variation which is crucial for the stability and robustness of Newton algorithms. We present numerical results in the case of two-dimensional acoustic scattering problems to illustrate the potential of the proposed procedure for reconstructing the full aperture of the FFP from very few noisy data such as backscattering synthetic measurements.

A cheapest stable nonconforming finite element method is presented for solving the incompressible flow in a square cavity without smoothing the corner singularities. The stable cheapest nonconforming finite element pair based on P1×P0 on rectangularmeshes [29] is employed with a minimal modification of the discontinuous Dirichlet data on the top boundary, where is the finite element space of piecewise constant pressures with the globally one-dimensional checker-board pattern subspace eliminated. The proposed Stokes elements have the least number of degrees of freedom compared to those of known stable Stokes elements. Three accuracy indications for our elements are analyzed and numerically verified. Also, various numerous computational results obtained by using our proposed element show excellent accuracy.

Here we investigate the kinematic transports of the defects in the nematic liquid crystal system by numerical experiments. The model is a shear flow case of the viscoelastic continuummodel simplified fromthe Ericksen-Leslie system. The numerical experiments are carried out by using a difference method. Based on these numerical experiments we find some interesting and important relationships between the kinematic transports and the characteristics of the flow. We present the development and interaction of the defects. These results are partly consistent with the observation from the experiments. Thus this scheme illustrates, to some extent, the kinematic effects of the defects.

How to effectively simulate the interaction between fluid and solid elements of different sizes remains to be challenging. The discrete element method (DEM) has been used to deal with the interactions between solid elements of various shapes and sizes, while the material point method (MPM) has been developed to handle the multiphase (solid-liquid-gas) interactions involving failure evolution. A combined MPM-DEM procedure is proposed to take advantage of both methods so that the interaction between solid elements and fluid particles in a container could be better simulated. In the proposed procedure, large solid elements are discretized by the DEM, while the fluid motion is computed using the MPM. The contact forces between solid elements and rigid walls are calculated using the DEM. The interaction between solid elements and fluid particles are calculated via an interfacial scheme within the MPM framework. With a focus on the boundary condition effect, the proposed procedure is illustrated by representative examples, which demonstrates its potential for a certain type of engineering problems.

In their tubelike phase, nanowire-adsorbed polymers exhibit strong structural similarities to morphologies known from single-walled carbon (hexagonal) and boron (triangular) nanotubes. Since boron/boron nitride tubes require some disorder for stability the triangular polymer tubes provide a closer analog to the carbon tubes. By means of computer simulations of both two and three dimensional versions of a coarse-grained bead-spring model for the polymers, we investigate their structural properties and make a detailed comparison with structures of carbon nanotubes.