Cancer spread is a dynamical process occurring not only in time but also in space which, for solid tumors at least, can be modeled quantitatively by reaction and diffusion equations with a bistable behavior: tumor cell colonization happens in a portion of tissue and propagates, but in some cases the process is stopped. Such a cancer proliferation/extintion dynamics is obtained in many mathematical models as a limit of complicated interacting biological fields. In this article we present a very basic model of cancer proliferation adopting the bistable equation for a single tumor cell dynamics. The reaction-diffusion theory is numerically and analytically studied and then extended in order to take into account dispersal effects in cancer progression in analogy with ecological models based on the porous medium equation. Possible implications of this approach for explanation and prediction of tumor development on the lines of existing studies on brain cancer progression are discussed. The potential role of continuum models in connecting the two predominant interpretative theories about cancer, once formalized in appropriate mathematical terms, is discussed.

In the present article, coarse grained Dissipative Particle Dynamics simulation with implementation of electrostatic interactions is developed in constant pressure and surface tension ensemble to elucidate how the antimicrobial peptide molecules affect bilayer cell membrane structure and kill bacteria. We find that peptides with different chemical-physical properties exhibit different membrane obstructing mechanisms. Peptide molecules can destroy vital functions of the affected bacteria by translocating across their membranes via worm-holes, or by associating with membrane lipids to form hydrophilic cores trapped inside the hydrophobic domain of the membranes. In the latter model, the affected membranes are strongly buckled, in accord with very recent experimental observations [G. E. Fantner et al., Nat. Nanotech., 5 (2010), pp. 280-285].

This paper is a continuation of our earlier work [SIAM J. Sci. Comput., 32(2010), pp. 2875-2907] in which a numerical moment method with arbitrary order of moments was presented. However, the computation may break down during the calculation of the structure of a shock wave with Mach number M0 ≥ 3. In this paper, we concentrate on the regularization of the moment systems. First, we apply the Maxwell iteration to the infinite moment system and determine the magnitude of each moment with respect to the Knudsen number. After that, we obtain the approximation of high order moments and close the moment systems by dropping some high-order terms. Linearization is then performed to obtain a very simple regularization term, thus it is very convenient for numerical implementation. To validate the new regularization, the shock structures of low order systems are computed with different shock Mach numbers.

We develop a framework for constructing mixed multiscale finite volume methods for elliptic equations with multiple scales arising from flows in porous media. Some of the methods developed using the framework are already known [20]; others are new. New insight is gained for the known methods and extra flexibility is provided by the new methods. We give as an example a mixed MsFV on uniform mesh in 2-D. This method uses novel multiscale velocity basis functions that are suited for using global information, which is often needed to improve the accuracy of the multiscale simulations in the case of continuum scales with strong non-local features. The method efficiently captures the small effects on a coarse grid. We analyze the new mixed MsFV and apply it to solve two-phase flow equations in heterogeneous porous media. Numerical examples demonstrate the accuracy and efficiency of the proposed method for modeling the flows in porous media with non-separable and separable scales.

This paper establishes relations between the stability and the high-order truncated corrections for modeling of the mass conservation equation with the two-relaxation-times (TRT) collision operator. First we propose a simple method to derive the truncation errors from the exact, central-difference type, recurrence equations of the TRT scheme. They also supply its equivalent three-time-level discretization form. Two different relationships of the two relaxation rates nullify the third (advection) and fourth (pure diffusion) truncation errors, for any linear equilibrium and any velocity set. However, the two relaxation times alone cannot remove the leading-order advection-d if fusion error, because of the intrinsic fourth-order numerical diffusion. The truncation analysis is carefully verified for the evolution of concentration waves with the anisotropic diffusion tensors. The anisotropic equilibrium functions are presented in a simple but general form, suitable for the minimal velocity sets and the d2Q9, d3Q13, d3Q15 and d3Q19 velocity sets. All anisotropic schemes are complemented by their exact necessary von Neumann stability conditions and equivalent finite-difference stencils. The sufficient stability conditions are proposed for the most stable (OTRT) family, which enables modeling at any Peclet numbers with the same velocity amplitude. The heuristic stability analysis of the fourth-order truncated corrections extends the optimal stability to larger relationships of the two relaxation rates, in agreement with the exact (one-dimensional) and numerical (multi-dimensional) stability analysis. A special attention is put on the choice of the equilibrium weights. By combining accuracy and stability predictions, several strategies for selecting the relaxation and free-tunable equilibrium parameters are suggested and applied to the evolution of the Gaussian hill.

We report an efficient phase field formalism to compute the stress distribution in polycrystalline materials with arbitrary elastic inhomogeneity and anisotropy The dependence of elastic stiffness tensor on grain orientation is taken into account, and the elastic equilibrium equation is solved using a spectral iterative perturbation method. We discuss its applications to computing residual stress distribution in systems containing arbitrarily shaped cavities and cracks (with zero elastic modulus) and to determining the effective elastic properties of polycrystals and multilayered composites.

We study the inverse problem of recovering the scatterer shape from the far-field pattern(FFP) in the presence of noise. Furthermore, only a discrete partial aperture is usually known. This problem is ill-posed and is frequently addressed using regularization. Instead, we propose to use a direct approach denoising the FFP using a filtering technique. The effectiveness of the technique is studied on a scatterer with the shape of the ellipse with a tower. The forward scattering problem is solved using the finite element method (FEM). The numerical FFP is additionally corrupted by Gaussian noise. The shape parameters are found based on a least-square error estimator. If ũ∞ is a perturbation of the FFP then we attempt to find Γ, the scatterer shape, which minimizes ∣∣ũ∞ − ũ∞∣∣ using the conjugate gradient method for the denoised FFP

The parallel implementation of MUPHY, a concurrent multiscale code for large-scale hemodynamic simulations in anatomically realistic geometries, for multi-GPU platforms is presented. Performance tests show excellent results, with a nearly linear parallel speed-up on up to 32GPUs and a more than tenfold GPU/CPU acceleration, all across the range of GPUs. The basic MUPHY scheme combines a hydrokinetic (Lattice Boltzmann) representation of the blood plasma, with a Particle Dynamics treatment of suspended biological bodies, such as red blood cells. To the best of our knowledge, this represents the first effort in the direction of laying down general design principles for multiscale/physics parallel Particle Dynamics applications in non-ideal geometries. This configures the present multi-GPU version of MUPHY as one of the first examples of a high-performance parallel code for multiscale/physics biofluidic applications in realistically complex geometries.

We present Path Integral Monte Carlo C code for calculation of quantum mechanical transition amplitudes for 1D models. The SPEEDUP C code is based on the use of higher-order short-time effective actions and implemented to the maximal order p=18 in the time of propagation (Monte Carlo time step), which substantially improves the convergence of discretized amplitudes to their exact continuum values. Symbolic derivation of higher-order effective actions is implemented in SPEEDUP Mathematica codes, using the recursive Schrödinger equation approach. In addition to the general 1D quantum theory, developed Mathematica codes are capable of calculating effective actions for specific models, for general 2D and 3D potentials, as well as for a general many-body theory in arbitrary number of spatial dimensions.

After setting a mixed formulation for the propagation of linearized water waves problem, we define its spectral element approximation. Then, in order to take into account unbounded domains, we construct absorbing perfectly matched layer for the problem. We approximate these perfectly matched layer by mixed spectral elements and show their stability using the “frozen coefficient” technique. Finally, numerical results will prove the efficiency of the perfectly matched layer compared to classical absorbing boundary conditions.

We describe and review non oscillatory residual distribution schemes that are rather natural extension of high order finite volume schemes when a special emphasis is put on the structure of the computational stencil. We provide their connections with standard stabilized finite element and discontinuous Galerkin schemes, show that their are really non oscillatory. We also discuss the extension to these methods to parabolic problems. We also draw some research perspectives.

In this paper, the high-order space-time discontinuous Galerkin cell vertex scheme (DG-CVS) developed by the authors for hyperbolic conservation laws is extended for time dependent diffusion equations. In the extension, the treatment of the diffusive flux is exactly the same as that for the advective flux. Thanks to the Riemann-solver-free and reconstruction-free features of DG-CVS, both the advective flux and the diffusive flux are evaluated using continuous information across the cell interface. As a result, the resulting formulation with diffusive fluxes present is still consistent and does not need any extra ad hoc techniques to cure the common “variational crime” problem when traditional DG methods are applied to diffusion problems. For this reason, DG-CVS is conceptually simpler than other existing DG-typed methods.

In this paper we show that entropy can be used within a functional for the stress relaxation time of solid materials to parametrise finite viscoplastic strain-hardening deformations. Through doing so the classical empirical recovery of a suitable irreversible scalar measure of work-hardening from the three-dimensional state parameters is avoided. The success of the proposed approach centres on determination of a rate-independent relation between plastic strain and entropy, which is found to be suitably simplistic such to not add any significant complexity to the final model. The result is sufficiently general to be used in combination with existing constitutive models for inelastic deformations parametrised by one-dimensional plastic strain provided the constitutive models are thermodynamically consistent. Here a model for the tangential stress relaxation time based upon established dislocation mechanics theory is calibrated for OFHC copper and subsequently integrated within a two-dimensional moving-mesh scheme. We address some of the numerical challenges that are faced in order to ensure successful implementation of the proposedmodel within a hydrocode. The approach is demonstrated through simulations of flyer-plate and cylinder impacts.

The purpose of this article is to summarize our recent progress in high-order and high accurate CFD methods for flow problems with complex grids as well as to discuss the engineering prospects in using these methods. Despite the rapid development of high-order algorithms in CFD, the applications of high-order and high accurate methods on complex configurations are still limited. One of the main reasons which hinder the widely applications of these methods is the complexity of grids. Many aspects which can be neglected for low-order schemes must be treated carefully for high-order ones when the configurations are complex. In order to implement high-order finite difference schemes on complex multi-block grids, the geometric conservation law and block-interface conditions are discussed. A conservative metric method is applied to calculate the grid derivatives, and a characteristic-based interface condition is employed to fulfil high-order multi-block computing. The fifth-order WCNS-E-5 proposed by Deng is applied to simulate flows with complex grids, including a double-delta wing, a transonic airplane configuration, and a hypersonic X-38 configuration. The results in this paper and the references show pleasant prospects in engineering-oriented applications of high-order schemes.

Numerical methods of a 3D multiphysics, two-phase transport model of proton exchange membrane fuel cell (PEMFC) is studied in this paper. Due to the coexistence of multiphase regions, the standard finite element/finite volume method may fail to obtain a convergent nonlinear iteration for a two-phase transport model of PEMFC [49,50]. By introducing Kirchhoff transformation technique and a combined finite element-upwind finite volume approach, we efficiently achieve a fast convergence and reasonable solutions for this multiphase, multiphysics PEMFC model. Numerical implementation is done by using a novel automated finite element/finite volume program generator (FEPG). By virtue of a high-level algorithm description language (script), component programming and human intelligence technologies, FEPG can quickly generate finite element/finite volume source code for PEMFC simulation. Thus, one can focus on the efficient algorithm research without being distracted by the tedious computer programming on finite element/finite volume methods. Numerical success confirms that FEPG is an efficient tool for both algorithm research and software development of a 3D, multiphysics PEMFC model with multicomponent and multiphase mechanism.

The study of interactions between a high-power laser and atoms has been one of the fundamental and interesting topics in strong field physics for decades. Based on a nonperturbative model, ten years ago, we developed a set of programs to facilitate the study of interactions between a circularly polarized laser and atomic hydrogen. These programs included only contribution from the bound states of the hydrogen atom. However, as the laser intensity increases, contribution from continuum states to the excitation and ionization processes becomes larger and can no longer be neglected. Furthermore, because the original code is not able to add this contribution directly due to its many disadvantages, a major upgrade of the code is required before including the contribution from continuum states in future. In this paper, first we deduce some important formulas for contribution of continuum states and present modifications and tests for the upgraded code in detail. Second we show some comparisons among new results, old results from the original codes and the available experimental data. Overall the new result agrees with experimental data well. Last we present our calculation of above-threshold ionization (ATI) rate and compare it with a pertuba-tive calculation. The comparison shows that our nonperturbative calculation can also produce ATI peak suppression.

This work concerns multiple-scattering problems for time-harmonic equations in a reference generic media. We consider scatterers that can be sources, obstacles or compact perturbations of the reference media. Our aim is to restrict the computational domain to small compact domains containing the scatterers. We use Robin-to-Robin (RtR) operators (in the most general case) to express boundary conditions for the interior problem. We show that one can always factorize the RtR map using only operators defined using single-scatterer problems. This factorization is based on a decomposition of the diffracted field, on the whole domain where it is defined. Assuming that there exists a good method for solving single-scatterer problems, it then gives a convenient way to compute RtR maps for a random number of scatterers.