In this work, we carry out an analytical and numerical investigation of travelling waves representing arced vegetation patterns on sloped terrains. These patterns are reported to appear also in ecosystems which are not water deprived; therefore, we study the hypothesis that their appearance is due to plant–soil negative feedback, namely due to biomass-(auto)toxicity interactions.

To this aim, we introduce a reaction-diffusion-advection model describing the dynamics of vegetation biomass and toxicity which includes the effect of sloped terrains on the spatial distribution of these variables. Our analytical investigation shows the absence of Turing patterns, whereas travelling waves (moving uphill in the slope direction) emerge. Investigating the corresponding dispersion relation, we provide an analytic expression for the asymptotic speed of the wave. Numerical simulations not only just confirm this analytical quantity but also reveal the impact of toxicity on the structure of the emerging travelling pattern.

Our analysis represents a further step in understanding the mechanisms behind relevant plants‘ spatial distributions observed in real life. In particular, since vegetation patterns (both stationary and transient) are known to play a crucial role in determining the underlying ecosystems’ resilience, the framework presented here allows us to better understand the emergence of such structures to a larger variety of ecological scenarios and hence improve the relative strategies to ensure the ecosystems’ resilience.

We consider a class of optimal control problems for measure-valued nonlinear transport equations describing traffic flow problems on networks. The objective is to minimise/maximise macroscopic quantities, such as traffic volume or average speed, controlling few agents, e.g. smart traffic lights and automated cars. The measure theoretic approach allows to study in a same setting local and non-local drivers interactions and to consider the control variables as additional measures interacting with the drivers distribution. We also propose a gradient descent adjoint-based optimisation method, obtained by deriving first-order optimality conditions for the control problem, and we provide some numerical experiments in the case of smart traffic lights for a 2–1 junction.

In this work, element free Galerkin (EFG) method is posed for solving nonlinear, reaction-diffusion systems which are often employed in mathematical modeling in developmental biology. A predicator-corrector scheme is applied, to avoid directly solving of coupled nonlinear systems. The EFG method employs the moving least squares (MLS) approximation to construct shape functions. This method uses only a set of nodal points and a geometrical description of the body to discretize the governing equation. No mesh in the classical sense is needed. However a background mesh is used for integration purpose. Numerical solutions for two cases of interest, the Schnakenberg model and the Gierer-Meinhardt model, in various regions is presented to demonstrate the effects of various domain geometries on the resulting biological patterns.

The paper presents a novel family of arbitrary high order multioperators approximations for convection, convection-diffusion or the fluid dynamics equations. As particular cases, the 16th- and 32th-order skew-symmetric multioperators for derivatives supplied by the 15th- and 31th-order dissipation multioperators are described. Their spectral properties and the comparative efficiency of the related schemes in the case of smooth solutions are outlined. The ability of the constructed conservative schemes to deal with discontinuous solutions is investigated. Several types of nonlinear hybrid schemes are suggested and tested against benchmark problems.

A parallel, high-order direct Discontinuous Galerkin (DDG) method has been developed for solving the three dimensional compressible Navier-Stokes equations on 3D hybrid grids. The most distinguishing and attractive feature of DDG method lies in its simplicity in formulation and efficiency in computational cost. The formulation of the DDG discretization for 3D Navier-Stokes equations is detailed studied and the definition of characteristic length is also carefully examined and evaluated based on 3D hybrid grids. Accuracy studies are performed to numerically verify the order of accuracy using flow problems with analytical solutions. The capability in handling curved boundary geometry is also demonstrated. Furthermore, an SPMD (single program, multiple data) programming paradigm based on MPI is proposed to achieve parallelism. The numerical results obtained indicate that the DDG method can achieve the designed order of accuracy and is able to deliver comparable results as the widely used BR2 scheme, clearly demonstrating that the DDG method provides an attractive alternative for solving the 3D compressible Navier-Stokes equations.

The motion and rotation of an ellipsoidal particle inside square tubes and rectangular tubes with the confinement ratio R/a∈(1.0,4.0) are studied by the lattice Boltzmann method (LBM), where R and a are the radius of the tube and the semi-major axis length of the ellipsoid, respectively. The Reynolds numbers (Re) up to 50 are considered. For the prolate ellipsoid inside square and rectangular tubes, three typical stable motion modes which depend on R/a are identified, namely, the kayaking mode, the tumbling mode, and the log-rolling mode are identified for the prolate spheroid. The diagonal plane strongly attracts the particle in square tubes with 1.2≤R/a<3.0. To explore the mechanism, some constrained cases are simulated. It is found that the tumbling mode in the diagonal plane is stable because the fluid force acting on the particle tends to diminish the small displacement and will bring it back to the plane. Inside rectangular tubes the particle will migrate to a middle plane between short walls instead of the diagonal plane. Through the comparisons between the initial unstable equilibrium motion state and terminal stable mode, it is seems that the particle tend to adopt the mode with smaller kinetic energy.

In this paper, we propose a new energy-preserving scheme and a new momentum-preserving scheme for the modified regularized long wave equation. The proposed schemes are designed by using the discrete variational derivative method and the finite volume element method. For comparison, we also propose a finite volume element scheme. The conservation properties of the proposed schemes are analyzed and we find that the energy-preserving scheme can precisely conserve the discrete total mass and total energy, the momentum-preserving scheme can precisely conserve the discrete total mass and total momentum, while the finite volume element scheme merely conserve the discrete total mass. We also analyze their linear stability property using the Von Neumann theory and find that the proposed schemes are unconditionally linear stable. Finally, we present some numerical examples to illustrate the effectiveness of the proposed schemes.

In this paper, we extend using the Runge-Kutta discontinuous Galerkin method together with the front tracking method to simulate the compressible two-medium flow on unstructured meshes. A Riemann problem is constructed in the normal direction in the material interfacial region, with the goal of obtaining a compact, robust and efficient procedure to track the explicit sharp interface precisely. Extensive numerical tests including the gas-gas and gas-liquid flows are provided to show the proposed methodologies possess the capability of enhancing the resolutions nearby the discontinuities inside of the single medium flow and the interfacial vicinities of the two-medium flow in many occasions.

We study the exciton diffusion in organic semiconductors from a macroscopic viewpoint. In a unified way, we conduct the equivalence analysis between Monte-Carlo method and diffusion equation model for photoluminescence quenching and photocurrent spectrum measurements, in both the presence and the absence of Förster energy transfer effect. Connections of these two models to Stern-Volmer method and exciton-exciton annihilation method are also specified for the photoluminescence quenching measurement.

The differential quadrature method (DQM) has been successfully used in a variety of fields. Similar to the conventional point discrete methods such as the collocation method and finite difference method, however, the DQM has some difficulty in dealing with singular functions like the Dirac-delta function. In this paper, two modifications are introduced to overcome the difficulty encountered in solving differential equations with Dirac-delta functions by using the DQM. The moving point load is work-equivalent to loads applied at all grid points and the governing equation is numerically integrated before it is discretized in terms of the differential quadrature. With these modifications, static behavior and forced vibration of beams under a stationary or a moving point load are successfully analyzed by directly using the DQM. It is demonstrated that the modified DQM can yield very accurate solutions. The compactness and computational efficiency of the DQM are retained in solving the partial differential equations with a time dependent Dirac-delta function.

Simulation of turbulent flows with shocks employing subgrid-scale (SGS) filtering may encounter a loss of accuracy in the vicinity of a shock. This paper addresses the accuracy improvement of LES of turbulent flows in two ways: (a) from the SGS model standpoint and (b) from the numerical method improvement standpoint. In an internal report, Kotov et al. ( “High Order Numerical Methods for large eddy simulation (LES) of Turbulent Flows with Shocks”, CTR Tech Brief, Oct. 2014, Stanford University), we performed a preliminary comparative study of different approaches to reduce the loss of accuracy within the framework of the dynamic Germano SGS model. The high order low dissipative method of Yee & Sjögreen (2009) using local flow sensors to control the amount of numerical dissipation where needed is used for the LES simulation. The considered improved dynamics model approaches include applying the one-sided SGS test filter of Sagaut & Germano (2005) and/or disabling the SGS terms at the shock location. For Mach 1.5 and 3 canonical shock-turbulence interaction problems, both of these approaches show a similar accuracy improvement to that of the full use of the SGS terms. The present study focuses on a five levels of grid refinement study to obtain the reference direct numerical simulation (DNS) solution for additional LES SGS comparison and approaches. One of the numerical accuracy improvements included here applies Harten's subcell resolution procedure to locate and sharpen the shock, and uses a one-sided test filter at the grid points adjacent to the exact shock location.

With the aim of solving in a four dimensional phase space a multi-scale Vlasov-Poisson system, we propose in a Particle-In-Cell framework a robust time-stepping method that works uniformly when the small parameter vanishes. As an exponential integrator, the scheme is able to use large time steps with respect to the typical size of the solution’s fast oscillations. In addition, we show numerically that the method has accurate long time behaviour and that it is asymptotic preserving with respect to the limiting Guiding Center system.

We discuss the development, verification, and performance of a GPU accelerated discontinuous Galerkin method for the solutions of two dimensional nonlinear shallow water equations. The shallow water equations are hyperbolic partial differential equations and are widely used in the simulation of tsunami wave propagations. Our algorithms are tailored to take advantage of the single instruction multiple data (SIMD) architecture of graphic processing units. The time integration is accelerated by local time stepping based on a multi-rate Adams-Bashforthscheme. A total variational bounded limiter is adopted for nonlinear stability of the numerical scheme. This limiter is coupled with a mass and momentum conserving positivity preserving limiter for the special treatment of a dry or partially wet element in the triangulation. Accuracy, robustness and performance are demonstrated with the aid of test cases. Furthermore, we developed a unified multi-threading model OCCA. The kernels expressed in OCCA model can be cross-compiled with multi-threading models OpenCL, CUDA, and OpenMP. We compare the performance of the OCCA kernels when cross-compiled with these models.

This study presents a numerical solution to the three-dimensional solute transport in heterogeneous media by using a layer-integrated approach. Omitting vertical spatial variation of soil and hydraulic properties within each layer, a three-dimensional solute transport can be simplified as a quasi-three-dimensional solute transport which couples a horizontal two-dimensional simulation and a vertical one-dimensional computation. The finite analytic numerical method was used to discretize the derived two-dimensional governing equation. A quadratic function was used to approximate the vertical one-dimensional concentration distribution in the layer to ensure the continuity of concentration and flux at the interface between the adjacent layers. By integration over each layer, a set of system of equations can be generated for a single column of vertical cells and solved numerically to give the vertical solute concentration profile. The solute concentration field was then obtained by solving all columns of vertical cells to achieve convergence with the iterative solution procedure. The proposed model was verified through examples from the published literatures including four verifications in terms of analytical and experimental cases. Comparison of simulation results indicates that the proposed model satisfies the solute concentration profiles obtained from experiments in time and space.

Based on the numerical evidences, an analytical expression of the Dirichlet-to-Neumann mapping in the form of infinite product was first conjectured for the one-dimensional characteristic Schrödinger equation with a sinusoidal potential in [Commun. Comput. Phys., 3(3): 641-658, 2008]. It was later extended for the general second-order characteristic elliptic equations with symmetric periodic coefficients in [J. Comp. Phys., 227: 6877-6894, 2008]. In this paper, we present a proof for this Dirichlet-to-Neumann mapping.

In [SIAM J. Sci. Comput., 35(2)(2013), A1049-A1072], a class of multi-domain hybrid DG and WENO methods for conservation laws was introduced. Recent applications of this method showed that numerical instability may encounter if the DG flux with Lagrangian interpolation is applied as the interface flux during the moment of conservative coupling. In this continuation paper, we present a more robust approach in the construction of DG flux at the coupling interface by using WENO procedures of reconstruction. Based on this approach, such numerical instability is overcome very well. In addition, the procedure of coupling a DG method with a WENO-FD scheme on hybrid meshes is disclosed in detail. Typical testing cases are employed to demonstrate the accuracy of this approach and the stability under the flexibility of using either WENO-FD flux or DG flux at the moment of requiring conservative coupling.

In this paper, we present a new type of Hermite weighted essentially non-oscillatory (HWENO) schemes for solving the Hamilton-Jacobi equations on the finite volume framework. The cell averages of the function and its first one (in one dimension) or two (in two dimensions) derivative values are together evolved via time approaching and used in the reconstructions. And the major advantages of the new HWENO schemes are their compactness in the spacial field, purely on the finite volume framework and only one set of small stencils is used for different type of the polynomial reconstructions. Extensive numerical tests are performed to illustrate the capability of the methodologies.

In [35,36], we presented an h-adaptive Runge-Kutta discontinuous Galerkin method using troubled-cell indicators for solving hyperbolic conservation laws. A tree data structure (binary tree in one dimension and quadtree in two dimensions) is used to aid storage and neighbor finding. Mesh adaptation is achieved by refining the troubled cells and coarsening the untroubled “children”. Extensive numerical tests indicate that the proposed h-adaptive method is capable of saving the computational cost and enhancing the resolution near the discontinuities. In this paper, we apply this h-adaptive method to solve Hamilton-Jacobi equations, with an objective of enhancing the resolution near the discontinuities of the solution derivatives. One- and two-dimensional numerical examples are shown to illustrate the capability of the method.

The numerical solution of a parabolic Volterra integro-differential equation with a memory term on a one-dimensional unbounded spatial domain is considered. A quasi-wavelet based numerical method is proposed to handle the spatial discretisation, the Crank-Nicolson scheme is used for the time discretisation, and second-order quadrature to approximate the integral term. Some numerical examples are presented to illustrate the efficiency and accuracy of this approach.

Discontinuities usually appear in solutions of nonlinear conservation laws even though the initial condition is smooth, which leads to great difficulty in computing these solutions numerically. The Runge-Kutta discontinuous Galerkin (RKDG) methods are efficient methods for solving nonlinear conservation laws, which are high-order accurate and highly parallelizable, and can be easily used to handle complicated geometries and boundary conditions. An important component of RKDG methods for solving nonlinear conservation laws with strong discontinuities in the solution is a nonlinear limiter, which is applied to detect discontinuities and control spurious oscillations near such discontinuities. Many such limiters have been used in the literature on RKDG methods. A limiter contains two parts, first to identify the “troubled cells”, namely, those cells which might need the limiting procedure, then to replace the solution polynomials in those troubled cells by reconstructed polynomials which maintain the original cell averages (conservation). [SIAM J. Sci. Comput., 26 (2005), pp. 995–1013.] focused on discussing the first part of limiters. In this paper, focused on the second part, we will systematically investigate and compare a few different reconstruction strategies with an objective of obtaining the most efficient and reliable reconstruction strategy. This work can help with the choosing of right limiters so one can resolve sharper discontinuities, get better numerical solutions and save the computational cost.