This paper analyzes an abstract two-level algorithm for hybridizable discontinuous Galerkin (HDG) methods in a unified fashion. We use an extended version of the Xu-Zikatanov (X-Z) identity to derive a sharp estimate of the convergence rate of the algorithm, and show that the theoretical results also are applied to weak Galerkin (WG) methods. The main features of our analysis are twofold: one is that we only need the minimal regularity of the model problem; the other is that we do not require the triangulations to be quasi-uniform. Numerical experiments are provided to confirm the theoretical results.

In two-phase flow simulations, a difficult issue is usually the treatment of surface tension effects. These cause a pressure jump that is proportional to the curvature of the interface separating the two fluids. Since the evaluation of the curvature incorporates second derivatives, it is prone to numerical instabilities. Within this work, the interface is described by a level-set method based on a discontinuous Galerkin discretization. In order to stabilize the evaluation of the curvature, a patch-recovery operation is employed. There are numerous ways in which this filtering operation can be applied in the whole process of curvature computation. Therefore, an extensive numerical study is performed to identify optimal settings for the patch-recovery operations with respect to computational cost and accuracy.

Free energy lattice Boltzmann methods are well suited for the simulation of two phase flow problems. The model for the interface is based on well understood physical grounds. In most cases a numerical interface is used instead of the physical one because of lattice resolution limitations. In this paper we present a framework where we can both follow the droplet behavior in a coarse scale and solve the interface in a fine scale simultaneously. We apply the method for the simulation of a droplet using an interface to diameter size ratio of 1 to 280. In a second simulation, a small droplet coalesces with a 42 times larger droplet producing on it only a small capillary wave that propagates and dissipates.

A new VMD plugin that interfaces with DelPhi to provide ensemble-averaged electrostatic calculations using the Poisson-Boltzmann equation is presented. The general theory and context of this approach are discussed, and examples of the plugin interface and calculations are presented. This new tool is applied to systems of current biological interest, obtaining the ensemble-averaged electrostatic properties of the two major influenza virus glycoproteins, hemagglutinin and neuraminidase, from explicitly solvated all-atom molecular dynamics trajectories. The differences between the ensemble-averaged electrostatics and those obtained from a single structure are examined in detail for these examples, revealing how the plugin can be a powerful tool in facilitating the modeling of electrostatic interactions in biological systems.

Moving mesh methods provide an efficient way of solving partial differential equations for which large, localised variations in the solution necessitate locally dense spatial meshes. In one-dimension, meshes are typically specified using the arclength mesh density function. This choice is well-justified for piecewise polynomial interpolants, but it is only justified for spectral methods when model solutions include localised steep gradients. In this paper, one-dimensional mesh density functions are presented which are based on a spatially localised measure of the bandwidth of the approximated model solution. In considering bandwidth, these mesh density functions are well-justified for spectral methods, but are not strictly tied to the error properties of any particular spatial interpolant, and are hence widely applicable. The bandwidth mesh density functions are illustrated in two ways. First, by applying them to Chebyshev polynomial approximation of two test functions, and second, through use in periodic spectral and finite-difference moving mesh methods applied to a number of model problems in acoustics. These problems include a heterogeneous advection equation, the viscous Burgers’ equation, and the Korteweg-de Vries equation. Simulation results demonstrate solution convergence rates that are up to an order of magnitude faster using the bandwidth mesh density functions than uniform meshes, and around three times faster than those using the arclength mesh density function.

We present a finite volume based cell-centered method for solving diffusion equations on three-dimensional unstructured grids with general tensor conduction. Our main motivation concerns the numerical simulation of the coupling between fluid flows and heat transfers. The corresponding numerical scheme is characterized by cell-centered unknowns and a local stencil. Namely, the scheme results in a global sparse diffusion matrix, which couples only the cell-centered unknowns. The space discretization relies on the partition of polyhedral cells into sub-cells and on the partition of cell faces into sub-faces. It is characterized by the introduction of sub-face normal fluxes and sub-face temperatures, which are auxiliary unknowns. A sub-cellbased variational formulation of the constitutive Fourier law allows to construct an explicit approximation of the sub-face normal heat fluxes in terms of the cell-centered temperature and the adjacent sub-face temperatures. The elimination of the sub-face temperatures with respect to the cell-centered temperatures is achieved locally at each node by solving a small and sparse linear system. This systemis obtained by enforcing the continuity condition of the normal heat flux across each sub-cell interface impinging at the node under consideration. The parallel implementation of the numerical algorithm and its efficiency are described and analyzed. The accuracy and the robustness of the proposed finite volumemethod are assessed bymeans of various numerical test cases.

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 importance of eliminating errors in grid-metric evaluation for high-order difference schemes has been widely recognized in recent years, and it is known from the proof by Vinokur and Yee (NASA TM 209598, 2000) that when conservative derivations of grid metric are used by Thomas, Lombard and Neier (AIAA J., 1978, 17(10) and J. Spacecraft and rocket, 1990, 27(2)), errors caused by metric evaluation could be eliminated by linear schemes when flux splitting is not considered. According to the above achievement, central schemes without the use of flux splitting could fulfill the requirement of error elimination. Difficulties will arise for upwind schemes to attain the objective when the splitting is considered. In this study, further investigations are made on three aspects: Firstly, an idea of central scheme decomposition is introduced, and the procedure to derive the central scheme is proposed to evaluate grid metrics only. Secondly, the analysis has been made on the requirement of flux splitting to acquire free-stream preservation, and a Lax-Friedrichs-type splitting scheme is proposed as an example. Discussions about current study with that by Nonomura et al. (Computers and Fluids, 2015, 107) have been made. Thirdly, for half-node- or mixed-type schemes, interpolations should be used to derive variables at half nodes. The requirement to achieve metric identity on this situation is analyzed and an idea of directionally consistent interpolation is proposed, which is manifested to be indispensable to avoid violations of metric identity and to eliminate metric-caused errors thereafter. Two numerical problems are tested, i.e., the free-stream and vortex preservation on wavy, largely randomized and triangular-like grids. Numerical results validate aforementioned theoretical outcomes.

We present a systematic derivation of a model based on the central moment lattice Boltzmann equation that rigorously maintains Galilean invariance of forces to simulate inertial frame independent flow fields. In this regard, the central moments, i.e. moments shifted by the local fluid velocity, of the discrete source terms of the lattice Boltzmann equation are obtained by matching those of the continuous full Boltzmann equation of various orders. This results in an exact hierarchical identity between the central moments of the source terms of a given order and the components of the central moments of the distribution functions and sources of lower orders. The corresponding source terms in velocity space are then obtained from an exact inverse transformation due to a suitable choice of orthogonal basis for moments. Furthermore, such a central moment based kinetic model is further extended by incorporating reduced compressibility effects to represent incompressible flow. Moreover, the description and simulation of fluid turbulence for full or any subset of scales or their averaged behavior should remain independent of any inertial frame of reference. Thus, based on the above formulation, a new approach in lattice Boltzmann framework to incorporate turbulence models for simulation of Galilean invariant statistical averaged or filtered turbulent fluid motion is discussed.

Red blood cells undergo substantial shape changes in vivo. Modeled as a viscoelastic capsule, their deformation and equilibrium behavior has been extensively studied. We consider how 2D capsules recover their shape, after having been deformed to ‘equilibrium’ behavior by shear flow. The fluid-structure interaction is modeled using the multiple-relaxation time lattice Boltzmann (LBM) and immersed boundary (IBM) methods. Characterizing the capsule’s shape recovery with the Taylor deformation parameter, we find that a single exponential decay model suffices to describe the recovery of a circular capsule. However, for biconcave capsules whose equilibrium behaviors are tank-treading and tumbling, we posit a two-part recovery, modeled with a pair of exponential decay functions. We consider how these two recovery modes depend on the capsule’s shear elasticity, membrane viscosity, and bending stiffness, along with the ratio of the viscosity of the fluid inside the capsule to the ambient fluid viscosity. We find that the initial recovery mode for a tank-treading biconcave capsule is dominated by shear elasticity and membrane viscosity. On the other hand, the latter recovery mode for both tumbling and tank-treading capsules, depends clearly on shear elasticity, bending stiffness, and the viscosity ratio.

A new algorithm, called boosted hybrid method, is proposed for the simulation of chemical reaction systems with scale-separation in time and disparity in species population. For such stiff systems, the algorithm can automatically identify scale-separation in time and slow down the fast reactions while maintaining a good approximation to the original effective dynamics. This technique is called boosting. As disparity in species population may still exist in the boosted system, we propose a hybrid strategy based on coarse-graining methods, such as the tau-leaping method, to accelerate the reactions among large population species. The combination of the boosting strategy and the hybrid method allow for an efficient and adaptive simulation of complex chemical reactions. The new method does not need a priori knowledge of the system and can also be used for systems with hierarchical multiple time scales. Numerical experiments illustrate the versatility and efficiency of the method.

Consider the time-harmonic acoustic scattering from an extended elastic body surrounded by a finite number of point-like obstacles in a fluid. We assume point source waves are emitted from arrayed transducers and the signals of scattered near-field data are recorded by receivers not far away from the scatterers (compared to the incident wavelength). The forward scattering can be modeled as an interaction problem between acoustic and elastic waves together with a multiple scattering problem between the extend solid and point scatterers. We prove a necessary and sufficient condition that can be used simultaneously to recover the shape of the extended elastic solid and to locate the positions of point scatterers. The essential ingredient in our analysis is the outgoing-to-incoming (OtI) operator applied to the resulting near-field response matrix (or operator). In the first part, we justify the MUSIC algorithm for locating point scatterers from near-field measurements. In the second part, we apply the factorization method, the continuous analogue of MUSIC, to the two-scale scattering problem for determining both extended and point scatterers. Numerical examples in 2D are demonstrated to show the validity and accuracy of our inversion algorithms.

By combining the characteristic method and the local discontinuous Galerkin method with carefully constructing numerical fluxes, variational formulations are established for time-dependent incompressible Navier-Stokes equations in ℝ2. The nonlinear stability is proved for the proposed symmetric variational formulation. Moreover, for general triangulations the priori estimates for the L2–norm of the errors in both velocity and pressure are derived. Some numerical experiments are performed to verify theoretical results.

The present paper provides a numerical investigation of the decoherence effect induced on a quantum heavy particle by the scattering with a light one. The time dependent two-particle Schrödinger equation is solved by means of a time-splitting method. The damping undergone by the non-diagonal terms of the heavy particle density matrix is estimated numerically as well as the error in the Joos-Zeh approximation formula.

This paper is devoted to the numerical approximation of a degenerate anisotropic elliptic problem. The numerical method is designed for arbitrary space-dependent anisotropy directions and does not require any specially adapted coordinate system. It is also designed to be equally accurate in the strongly and the mildly anisotropic cases. The method is applied to the Euler-Lorentz system, in the drift-fluid limit. This system provides a model for magnetized plasmas.

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].

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.

This study mainly focused on the key technologies, the photon dose calculation based on the Monte Carlo Finite-Size Pencil Beam (MCFSPB) model in the Accurate Radiotherapy System (ARTS). In the MCFSPB model, the acquisition of pencil beam kernel is one of the most important technologies. In this study, by analyzing the demerits of the clinical pencil beam dose calculation methods, a new pencil beam kernel model was developed based on the Monte Carlo (MC) simulation and the technology of medical accelerator energy spectrum reconstruction. which greatly improved the accuracy of calculated result. According to the axial symmetry principle, only part of simulation results was used for the data of pencil beam kernel, which greatly reduced the data quantity of the pencil beam and reduced calculated time. Based on the above studies, the MCFSPB method was designed and implemented by the Visual C++ development tool. With several tests including the comparisons among the American Association of Physicists in Medicine (AAPM) No. 55 Report sample and the ion chamber measurement of lung-simulating inhomogeneous phantom in clinical treatment plan, the results showed that the maximum error of most calculated point was less than 0.5% in the homogeneous phantom and less than 3% in the heterogeneous phantom. This method met the clinical criteria, and would be expected to be used as a fast and accurate dose engine for clinic TPS.

We present a new numerical method to approximate the solutions of an Euler-Poisson model, which is inherent to astrophysical flows where gravity plays an important role. We propose a discretization of gravity which ensures adequate coupling of the Poisson and Euler equations, paying particular attention to the gravity source term involved in the latter equations. In order to approximate this source term, its discretization is introduced into the approximate Riemann solver used for the Euler equations. A relaxation scheme is involved and its robustness is established. The method has been implemented in the software HERACLES [29] and several numerical experiments involving gravitational flows for astrophysics highlight the scheme.

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.