A numerical method is presented for the computation of externally forced Stokes flows bounded by the plane z=0 and satisfying periodic boundary conditions in the x and y directions. The motivation for this work is the simulation of flows generated by cilia, which are hair-like structures attached to the surface of cells that generate flows through coordinated beating. Large collections of cilia on a surface can be modeled using a doubly-periodic domain. The approach presented here is to derive a regularized version of the fundamental solution of the incompressible Stokes equations in Fourier space for the periodic directions and physical space for the z direction. This analytical expression for û(k,m;z) can then be used to compute the fluid velocity u(x,y,z) via a two-dimensional inverse fast Fourier transform for any fixed value of z. Repeating the computation for multiple values of z leads to the fluid velocity on a uniform grid in physical space. The zero-flow condition at the plane z=0 is enforced through the use of images. The performance of the method is illustrated by numerical examples of particle transport by nodal cilia, which verify optimal particle transport for parameters consistent with previous studies. The results also show that for two cilia in the periodic box, out-of-phase beating produces considerablemore particle transport than in-phase beating.

Dynamics and instability of a vortex ring impinging on a wall were investigated by means of large eddy simulation for two vortex core thicknesses corresponding to thin and thick vortex rings. Various fundamental mechanisms dictating the flow behaviors, such as evolution of vortical structures, formation of vortices wrapping around vortex rings, instability and breakdown of vortex rings, and transition from laminar to turbulent state, have been studied systematically. The evolution of vortical structures is elucidated and the formation of the loop-like and hair-pin vortices wrapping around the vortex rings (called briefly wrapping vortices) is clarified. Analysis of the enstrophy of wrapping vortices and turbulent kinetic energy (TKE) in flow field indicates that the formation and evolution of wrapping vortices are closely associated with the flow transition to turbulent state. It is found that the temporal development of wrapping vortices and the growth rate of axial flow generated around the circumference of the core region for the thin ring are faster than those for the thick ring. The azimuthal instabilities of primary and secondary vortex rings are analyzed and the development of modal energies is investigated to reveal the flow transition to turbulent state. The modal energy decay follows a characteristic –5/3 power law, indicating that the vortical flow has become turbulence. Moreover, it is identified that the TKE with a major contribution of the azimuthal component is mainly distributed in the core region of vortex rings. The results obtained in this study provide physical insight of the mechanisms relevant to the vortical flow evolution from laminar to turbulent state.

An alternate BGK type formulation of the Enskog equation has been recently proposed. It was shown that the new model has a valid H-theorem and correct thermal conductivity. We propose Lattice Boltzmann (LB) formulation of this new Enskog-BGK model. The molecular nature of the model is verified in case of shear flow by comparing the predicted normal stress behavior by the current model with the prediction of molecular dynamics simulations. We extend the model for multiphase flow by incorporating attractive part as Vlasov type force. To validate multiphase formulation, the results of 3D simulations of a condensing bubble in a periodic box are presented.

In this paper, an immersed interface method is presented to simulate the dynamics of inextensible interfaces in an incompressible flow. The tension is introduced as an augmented variable to satisfy the constraint of interface inextensibility and the resulting augmented system is solved by the GMRES method. In this work, the arclength of the interface is locally and globally conserved as the enclosed region undergoes deformation. The forces at the interface are calculated from the configuration of the interface and the computed augmented variable, and then applied to the fluid through the related jump conditions. The governing equations are discretized on a MAC grid via a second-order finite difference scheme which incorporates jump contributions and solved by the conjugate gradient Uzawa-type method. The proposed method is applied to several examples including the deformation of a liquid capsule with inextensible interfaces in a shear flow. Numerical results reveal that both the area enclosed by interface and arclength of interface are conserved well simultaneously. These provide further evidence on the capability of the present method to simulate incompressible flows involving inextensible interfaces.

We propose a mathematically rigorous method to measure the spontaneous curvature of a bilayer membrane by molecular dynamics (MD) simulation, which provides description of the molecular mechanisms that cause the spontaneous curvature. As a main result, for the membrane setup investigated, the spontaneous curvature is proved to be a constant plus twice the mean curvature of the membrane in its tensionless ground state. The spontaneous curvature due to the built-in transbilayer asymmetry of the membrane in terms of lipid shape is studied by the proposed method. A linear dependence of the spontaneous curvature with respect to the head-bead diameter difference and the lipid mixing ratio is discovered. The consistency with the theoretical results provides evidence supporting the validity of our method.

In this work, we introduce an IMEX discontinuous Galerkin solver for the weakly compressible isentropic Euler equations. The splitting needed for the IMEX temporal integration is based on the recently introduced reference solution splitting [32, 52], which makes use of the incompressible solution. We show that the overall method is asymptotic preserving. Numerical results show the performance of the algorithm which is stable under a convective CFL condition and does not show any order degradation.

A coupled model, capable of simulating transonic flow, solid heat conduction, species transport, and gas radiation, is developed that provides better computational treatment of infrared radiation from hot exhaust nozzles. The modeling of gas radiation is based on a statistical narrow-band correlated-k analysis, whose parameters are deduced from the HITEMP line-by-line database. To improve computational efficiency, several methods are employed. A mixed analytical-numerical algorithm is described for the stiffness of the two-equation turbulence model and an alternating direction implicit pretreatment for the ill-conditioned matrix appearing in the coupled problem of flow and solid heat conduction. Moreover, an improved multigrid method and a symmetry plane treatment of the radiation transfer-energy equations are also introduced. Four numerical simulations are given to confirm the efficiency and accuracy of the numerical method. Finally, an account of the aerothermodynamics and infrared characteristics for two types of nozzles are presented. The infrared radiation intensity of the Chevron ejecting nozzle is clearly smaller than that of the common axisymmetric ejecting nozzle. All computations can be performed on a personal computer.

This paper presents a parallel algorithm for finding the smallest eigenvalue of a family of Hankel matrices that are ill-conditioned. Such matrices arise in random matrix theory and require the use of extremely high precision arithmetic. Surprisingly, we find that a group of commonly-used approaches that are designed for high efficiency are actually less efficient than a direct approach for this class of matrices. We then develop a parallel implementation of the algorithm that takes into account the unusually high cost of individual arithmetic operations. Our approach combines message passing and shared memory, achieving near-perfect scalability and high tolerance for network latency. We are thus able to find solutions for much larger matrices than previously possible, with the potential for extending this work to systems with greater levels of parallelism. The contributions of this work are in three areas: determination that a direct algorithm based on the secant method is more effective when extreme fixed-point precision is required than are the algorithms more typically used in parallel floating-point computations; the particular mix of optimizations required for extreme precision large matrix operations on a modern multi-core cluster, and the numerical results themselves.

Recent studies on applications of the lattice Boltzmann method (LBM) and the finite-difference lattice Boltzmann method (FDLBM) to velocity slip simulations are mostly on one-dimensional (1D) problems such as a shear flow between parallel plates. Applications to a 2D problem may raise new issues. The author performed numerical simulations of rotational slip flow in coaxial cylinders as an example of 2D problem. Two types of 2D models were used. The first were multi-speed FDLBM models proposed by the author. The second was a standard LBM, the D2Q9 model. The simulations were performed applying a finite difference scheme to both the models. The study had two objectives. The first was to investigate the accuracies of LBM and FDLBM on applications to rotational slip flow. The second was to obtain an experience on application of the cylindrical coordinate system. The FDLBM model with 8 directions and the D2Q9 model showed an anisotropic flow pattern when the relaxation time constant or the Knudsen number was large. The FDLBM model with 24 directions showed accurate results even at large Knudsen numbers.

This paper develops Runge-Kutta PK -based central discontinuous Galerkin (CDG) methods with WENO limiter for the one- and two-dimensional special relativistic hydrodynamical (RHD) equations, K = 1,2,3. Different from the non-central DG methods, the Runge-Kutta CDG methods have to find two approximate solutions defined on mutually dual meshes. For each mesh, the CDG approximate solutions on its dual mesh are used to calculate the flux values in the cell and on the cell boundary so that the approximate solutions on mutually dual meshes are coupled with each other, and the use of numerical flux will be avoided. The WENO limiter is adaptively implemented via two steps: the “troubled” cells are first identified by using a modified TVB minmod function, and then the WENO technique is used to locally reconstruct new polynomials of degree (2K+1) replacing the CDG solutions inside the “troubled” cells by the cell average values of the CDG solutions in the neighboring cells as well as the original cell averages of the “troubled” cells. Because the WENO limiter is only employed for finite “troubled” cells, the computational cost can be as little as possible. The accuracy of the CDG without the numerical dissipation is analyzed and calculation of the flux integrals over the cells is also addressed. Several test problems in one and two dimensions are solved by using our Runge-Kutta CDG methods with WENO limiter. The computations demonstrate that our methods are stable, accurate, and robust in solving complex RHD problems.

Consider the scattering of a time-harmonic acoustic incident wave by a bounded, penetrable, and isotropic elastic solid, which is immersed in a homogeneous compressible air or fluid. The paper concerns the numerical solution for such an acoustic-elastic interaction problem in three dimensions. An exact transparent boundary condition (TBC) is developed to reduce the problem equivalently into a boundary value problem in a bounded domain. The perfectly matched layer (PML) technique is adopted to truncate the unbounded physical domain into a bounded computational domain. The well-posedness and exponential convergence of the solution are established for the truncated PML problem by using a PML equivalent TBC. An a posteriori error estimate based adaptive finite element method is developed to solve the scattering problem. Numerical experiments are included to demonstrate the competitive behavior of the proposed method.

In the paper, we focus on atom diffusion behavior in Ni-based superalloys, which have important applications in the aero-industry. Specifically, the expressions of the key physical parameter – transition rate (jump rate) in the diffusion can be given from the diffusion theory in solids and the kinetic Monte Carlo (KMC) method, respectively. The transition rate controls the diffusion process and is directly related to the energy of vacancy formation and the energy of migration of atom from density functional theory (DFT). Moreover, from the KMC calculations, the diffusion coefficients for Ni and Al atoms in the γ phase (Ni matrix) and the γʹ phase (intermetallic compound Ni3Al) of the superalloy have been obtained. We propose a strategy of time stepping to deal with the multi-time scale issues. In addition, the influence of temperature and Al concentration on diffusion in dilute alloys is also reported.

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.

In this paper, we study the Camassa-Holm equation and the Degasperis-Procesi equation. The two equations are in the family of integrable peakon equations, and both have very rich geometric properties. Based on these geometric structures, we construct the geometric numerical integrators for simulating their soliton solutions. The Camassa-Holm equation and the Degasperis-Procesi equation have many common properties, however they also have the significant difference, for example there exist the shock wave solutions for the Degasperis-Procesi equation. By using the symplectic Fourier pseudo-spectral integrator, we simulate the peakon solutions of the two equations. To illustrate the smooth solitons and shock wave solutions of the DP equation, we use the splitting technique and combine the composition methods. In the numerical experiments, comparisons of these two kinds of methods are presented in terms of accuracy, computational cost and invariants preservation.

The bubble packing method can generate high-quality node sets in simple and complex domains. However, its efficiency remains to be improved. This study is a part of an ongoing effort to introduce several acceleration schemes to reduce the cost of simulation. Firstly, allow the viscosity coefficient c in the bubble governing equations to change according the coordinate of the bubble which are defined separately as odd and normal bubbles, and meanwhile with the saw-shape relationship with time or iterations. Then, in order to relieve the over crowded initial bubble placement, two coefficients w1 and w2 are introduced to modify the insertion criterion. The range of those two coefficients are discussed to be w1 = 1, w2 ∈ [0.5,0.8]. Finally, a self-adaptive termination condition is logically set when the stable system equilibrium is achieved. Numerical examples illustrate that the computing cost can significantly decrease by roughly 80% via adopting various combination of proper schemes (except the uniform placement example), and the average qualities of corresponding Delaunay triangulation substantially exceed 0.9. It shows that those strategies are efficient and can generate a node set with high quality.

The Fulde-Ferrell-Larkin-Ovchinnikov (FFLO) state is the superconducting phase for which the Cooper pairs have a non-zero total momentum, depending on the splitting of the Fermi surface sheets for electrons with opposite spin. In infinite systems the momentum is a continuous function of the temperature. In this paper, we have shown how the finite size of the system, through the discretized geometry of the Fermi surface, affects the physical properties of the FFLO state by introducing discontinuities in the Cooper pair momentum. Our calculation in an isotropic system show that the superconducting state with two opposite Cooper pair momenta is more stable than state with one momentum also in nano-size systems, where finite size effects play a crucial role.

In this paper, the numerical error of two widely used methods for remapping of discrete quantities from one computational mesh to another is investigated. We compare the intuitive, but resource intensive method utilizing intersections of computational cells with the faster and simpler swept-region-based method. Both algorithms are formally second order accurate, however, they are known to produce slightly different quantity profiles in practical applications. The second-order estimate of the error formula is constructed algebraically for both algorithms so that their local accuracy can be evaluated. This general estimate is then used to assess the dependence of the performance of both methods on parameters such as the second derivatives of the remapped distribution, mesh geometry or mesh movement. Due to the complexity of such analysis, it is performed on a set of simplified elementary mesh patterns such as cell corner expansion, rotation or shear. On selected numerical tests it is demonstrated that the swept-based method can distort a symmetric quantity distribution more substantially than the intersection-based approach when the computational mesh moves in an unsuitable direction.

In plasma physics domain, the electron transport is described with the Fokker-Planck-Landau equation. The direct numerical solution of the kinetic equation is usually intractable due to the large number of independent variables. That is why we propose in this paper a new model whose derivation is based on an angular closure in the phase space and retains only the energy of particles as kinetic dimension. To find a solution compatible with physics conditions, the closure of the moment system is obtained under a minimum entropy principle. This model is proved to satisfy the fundamental properties like a H theorem. Moreover an entropic discretization in the velocity variable is proposed on the semi-discrete model. Finally, we validate on numerical test cases the fundamental properties of the full discrete model.

In this paper we describe a new pseudo-spectral method to solve numerically two and three-dimensional nonlinear diffusion equations over unbounded domains, taking Hermite functions, sinc functions, and rational Chebyshev polynomials as basis functions. The idea is to discretize the equations by means of differentiation matrices and to relate them to Sylvester-type equations by means of a fourth-order implicit-explicit scheme, being of particular interest the treatment of three-dimensional Sylvester equations that we make. The resulting method is easy to understand and express, and can be implemented in a transparent way by means of a few lines of code. We test numerically the three choices of basis functions, showing the convenience of this new approach, especially when rational Chebyshev polynomials are considered.

One viable approach to the study of haemodynamics is to numerically model this flow behavior in normal and stenosed arteries. The blood is either treated as Newtonian or non-Newtonian fluid and the flow is assumed to be pulsating, while the arteries can be modeled by constricted tubes with rigid or elastic wall. Such a task involves formulation and development of a numerical method that could at least handle pulsating flow of Newtonian and non-Newtonian fluid through tubes with and without constrictions where the boundary is assumed to be inelastic or elastic. As a first attempt, the present paper explores and develops a time-accurate finite difference lattice Boltzmann method (FDLBM) equipped with an immersed boundary (IB) scheme to simulate pulsating flow in constricted tube with rigid walls at different Reynolds numbers. The unsteady flow simulations using a time-accurate FDLBM/IB numerical scheme is validated against theoretical solutions and other known numerical data. In the process, the performance of the time-accurate FDLBM/IB for a model blood flow problem and the ease with which the no-slip boundary condition can be correctly implemented is successfully demonstrated.