Numerical methods are developed to simulate the wave propagation in heterogeneous 2D fluid/poroelastic media. Wave propagation is described by the usual acoustics equations (in the fluid medium) and by the low-frequency Biot’s equations (in the porous medium). Interface conditions are introduced to model various hydraulic contacts between the two media: open pores, sealed pores, and imperfect pores. Well-posedness of the initial-boundary value problem is proven. Cartesian grid numerical methods previously developed in porous heterogeneous media are adapted to the present context: a fourth-order ADER scheme with Strang splitting for time- marching; a space-time mesh-refinement to capture the slow compressional wave predicted by Biot’s theory; and an immersed interface method to discretize the interface conditions and to introduce a subcell resolution. Numerical experiments and comparisons with exact solutions are proposed for the three types of interface conditions, demonstrating the accuracy of the approach.

We present an efficient algorithm for calculating the minimum energy path (MEP) and energy barriers between local minima on a multidimensional potential energy surface (PES). Such paths play a central role in the understanding of transition pathways between metastable states. Our method relies on the original formulation of the string method [Phys. Rev. B, 66,052301 (2002)], i.e. to evolve a smooth curve along a direction normal to the curve. The algorithm works by performing minimization steps on hyperplanes normal to the curve. Therefore the problem of finding MEP on the PES is remodeled as a set of constrained minimization problems. This provides the flexibility of using minimization algorithms faster than the steepest descent method used in the simplified string method [J. Chem. Phys., 126(16), 164103 (2007)]. At the same time, it provides a more direct analog of the finite temperature string method. The applicability of the algorithm is demonstrated using various examples.

Velocity of fluid flow in underground porous media is 6~12 orders of magnitudes lower than that in pipelines. If numerical errors are not carefully controlled in this kind of simulations, high distortion of the final results may occur [1–4]. To fit the high accuracy demands of fluid flow simulations in porous media, traditional finite difference methods and numerical integration methods are discussed and corresponding high-accurate methods are developed. When applied to the direct calculation of full-tensor permeability for underground flow, the high-accurate finite difference method is confirmed to have numerical error as low as 10–5% while the high-accurate numerical integration method has numerical error around 0%. Thus, the approach combining the high-accurate finite difference and numerical integration methods is a reliable way to efficiently determine the characteristics of general full-tensor permeability such as maximum and minimum permeability components, principal direction and anisotropic ratio.

Realization of the Shan-Chen multiphase flow lattice Boltzmann model is considered in the framework of the higher-order Galilean invariant lattices. The present multiphase lattice Boltzmann model is used in two-dimensional simulation of droplet collisions at high Weber numbers. Results are found to be in a good agreement with experimental findings.

We propose a finite-difference ghost-point approach for the numerical solution of Cauchy-Navier equations in linear elasticity problems on arbitrary unbounded domains. The technique is based on a smooth coordinate transformation, which maps an unbounded domain into a unit square. Arbitrary geometries are defined by suitable level-set functions. The equations are discretized by classical nine-point stencil on interior points, while boundary conditions and high order reconstructions are used to define the field variables at ghost-points, which are grid nodes external to the domain with a neighbor inside the domain. The linear system arising from such discretization is solved by a multigrid strategy. The approach is then applied to solve elasticity problems in volcanology for computing the displacement caused by pressure sources. The method is suitable to treat problems in which the geometry of the source often changes (explore the effects of different scenarios, or solve inverse problems in which the geometry itself is part of the unknown), since it does not require complex re-meshing when the geometry is modified. Several numerical tests are successfully performed, which asses the effectiveness of the present approach.

Two fundamental facts of the modern wave turbulence theory are 1) existence of power energy spectra in k-space, and 2) existence of “gaps” in this spectra corresponding to the resonance clustering. Accordingly, three wave turbulent regimes are singled out: kinetic, described by wave kinetic equations and power energy spectra; discrete, characterized by resonance clustering; and mesoscopic, where both types of wave field time evolution coexist. In this review paper we present the results on integrable dynamics of resonance clusters appearing in discrete and mesoscopic wave turbulent regimes. Using a novel method based on the notion of dynamical invariant we show that some of the frequently met clusters are integrable in quadratures for arbitrary initial conditions and some others-only for particular initial conditions. We also identify chaotic behaviour in some cases. Physical implications of the results obtained are discussed.

The method of fundamentalsolutions (MFS)is known as aneffective boundary meshless method. However, the formulation of the MFS results in a dense and extremely ill-conditioned matrix. In this paper we investigate the MFS for solving large-scale problems for the nonhomogeneous modified Helmholtz equation. The key idea is to exploit the exponential decay of the fundamental solution of the modified Helmholtz equation, and consider a sparse or diagonal matrix instead of the original dense matrix. Hence, the homogeneous solution can be obtained efficiently and accurately. A standard two-step solution process which consists of evaluating the particular solution and the homogeneous solution is applied. Polyharmonic spline radial basis functions are employed to evaluate the particular solution. Five numerical examples in irregular domains and a large number of boundary collocation points are presented to show the simplicity and effectiveness of our approach for solving large-scale problems.

In this paper, an approach combining the DG method in space with CG method in time (CG-DG method) is developed to solve time-dependent Maxwell's equations when meta-materials are involved. Both the unconditional L2-stability and error estimate of order are obtained when polynomials of degree at most r is used for the temporal discretization and at most k for the spatial discretization. Numerical results in 3D are given to validate the theoretical results.

A weak Galerkin discretization of the boundary value problem of a general anisotropic diffusion problem is studied for preservation of the maximum principle. It is shown that the direct application of the M-matrix theory to the stiffness matrix of the weak Galerkin discretization leads to a strong mesh condition requiring all of the mesh dihedral angles to be strictly acute (a constant-order away from 90 degrees). To avoid this difficulty, a reduced system is considered and shown to satisfy the discrete maximum principle under weaker mesh conditions. The discrete maximum principle is then established for the full weak Galerkin approximation using the relations between the degrees of freedom located on elements and edges. Sufficient mesh conditions for both piecewise constant and general anisotropic diffusion matrices are obtained. These conditions provide a guideline for practical mesh generation for preservation of the maximum principle. Numerical examples are presented.

A novel full Eulerian fluid-elastic membrane coupling method on the fixed Cartesian coordinate mesh is proposed within the framework of the volume-of-fluid approach. The present method is based on a full Eulerian fluid-(bulk) structure coupling solver (Sugiyama et al., J. Comput. Phys., 230 (2011) 596-627), with the bulk structure replaced by elastic membranes. In this study, a closed membrane is consid-ered, and it is described by a volume-of-fluid or volume-fraction information generally called VOF function. A smoothed indicator (or characteristic) function is introduced as a phase indicator which results in a smoothed VOF function. This smoothed VOF function uses a smoothed delta function, and it enables a membrane singular force to be incorporated into a mixture momentum equation. In order to deal with a membrane deformation on the Eulerian mesh, a deformation tensor is introduced and updated within a compactly supported region near the interface. Both the neo-Hookean and the Skalak models are employed in the numerical simulations. A smoothed (and less dissipative) interface capturing method is employed for the advection of the VOF function and the quantities defined on the membrane. The stability restriction due to membrane stiffness is relaxed by using a quasi-implicit approach. The present method is validated by using the spherical membrane deformation problems, and is applied to a pressure-driven flow with the biconcave membrane capsules (red blood cells).

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].

A localized flexible airfoil at low Reynolds numbers is modeled and the aerodynamic performance is analyzed numerically. With characteristic based split scheme, a fluid solver for two dimensional incompressible Navier-Stokes equations is developed under the ALE framework, coupled with the theory of shallow arch, which is approximated by Galerkin method. Further, the interactions between the unsteady flow and the shallow arch are studied in detail. In particular, the effect of the self-excited vibration of the structure on aerodynamic performance of the airfoil is investigated deeply at various angles of attack. The results show that the lift-to-drag ratio has been increased greatly compared with the rigid airfoil. Finally, the relationship between the self-excited vibration and the evolution of the flow is analyzed using FFT tools.

We study efficient spectral-collocation and continuation methods (SCCM) for rotating two-component Bose-Einstein condensates (BECs) and rotating two-component BECs in optical lattices, where the second kind Chebyshev polynomials are used as the basis functions for the trial function space. A novel two-parameter continuation algorithm is proposed for computing the ground state and first excited state solutions of the governing Gross-Pitaevskii equations (GPEs), where the classical tangent vector is split into two constraint conditions for the bordered linear systems. Numerical results on rotating two-component BECs and rotating two-component BECs in optical lattices are reported. The results on the former are consistent with the published numerical results.

We apply the immersed boundary (or IB) method to simulate deformation and detachment of a periodic array of wall-bounded biofilm colonies in response to a linear shear flow. The biofilm material is represented as a network of Hookean springs that are placed along the edges of a triangulation of the biofilm region. The interfacial shear stress, lift and drag forces acting on the biofilm colony are computed by using fluid stress jump method developed by Williams, Fauci and Gaver [Disc. Con-tin. Dyn. Sys. B 11(2):519–540, 2009], with a modified version of their exclusion filter. Our detachment criterion is based on the novel concept of an averaged equivalent continuum stress tensor defined at each IB point in the biofilm which is then used to determine a corresponding von Mises yield stress; wherever this yield stress exceeds a given critical threshold the connections to that node are severed, thereby signalling the onset of a detachment event. In order to capture the deformation and detachment behaviour of a biofilm colony at different stages of growth, we consider a family of four biofilm shapes with varying aspect ratio. For each aspect ratio, we varied the spacing between colonies to investigate role of spatial clustering in offering protection against detachment. Our numerical simulations focus on the behaviour of weak biofilms (with relatively low yield stress threshold) and investigate features of the fluid-structure interaction such as locations of maximum shear and increased drag. The most important conclusions of this work are: (a) reducing the spacing between colonies reduces drag by from 50 to 100% and alters the interfacial shear stress profile, suggesting that even weak biofilms may be able to grow into tall structures because of the protection they gain from spatial proximity with other colonies; (b) the commonly employed detachment strategy in biofilm models based only on interfacial shear stress can lead to incorrect or inaccurate results when applied to the study of shear induced detachment of weak biofilms. Our detachment strategy based on equivalent continuum stresses provides a unified and consistent IB framework that handles both sloughing and erosion modes of biofilm detachment, and is consistent with strategies employed in many other continuum based biofilm models.

Local approximate radiation boundary conditions of optimal efficiency for the convective wave equation and the linearized Euler equations in waveguide geometry are formulated, analyzed, and tested. The results extend and improve for the convective case the general formulation of high-order local radiation boundary condition sequences for anisotropic scalar equations developed in [4].

A quasi non-overlapping hybrid scheme that combines the finite-difference time-domain (FDTD) method and the finite-element time-domain (FETD) method with nonconforming meshes is developed for time-domain solutions of Maxwell’s equations. The FETD method uses mixed-order basis functions for electric and magnetic fields, while the FDTD method uses the traditional Yee’s grid; the two methods are joined by a buffer zone with the FETD method and the discontinuous Galerkin method is used for the domain decomposition in the FETD subdomains. The main features of this technique is that it allows non-conforming meshes and an arbitrary numbers of FETD and FDTD subdomains. The hybrid method is completely stable for the time steps up to the stability limit for the FDTD method and FETD method. Numerical results demonstrate the validity of this technique.

Many molecular events are associated with small or large conformational changes occurring in the corresponding proteins. Modeling such changes is a challenge and requires significant amount of computing time. From point of view of electrostatics, these changes can be viewed as a reorganization of local charges and dipoles in response to the changes of the electrostatic field, if the cause is insertion or deletion of a charged amino acid. Here we report a large scale investigation of modeling the changes of the folding energy due to single mutations involving charged group. This allows the changes of the folding energy to be considered mostly electrostatics in origin and to be calculated with DelPhi assigning residue-specific value of the internal dielectric constant of protein. The predicted energy changes are benchmarked against experimentally measured changes of the folding energy on a set of 257 single mutations. The best fit between experimental values and predicted changes is used to find out the effective value of the internal dielectric constant for each type of amino acid. The predicted folding free energy changes with the optimal, amino acid specific, dielectric constants are within RMSD=0.86 kcal/mol from experimentally measured changes.

Motivated by the magneto hydrodynamic (MHD) simulation for Tokamaks with Isogeometric analysis, we present splines defined over a rectangular mesh with a complex topological structure, i.e., with extraordinary vertices. These splines are piecewise polynomial functions of bi-degree (d,d) and parameter continuity. And we compute their dimension and exhibit basis functions called Hermite bases for bicubic spline spaces. We investigate their potential applications for solving partial differential equations (PDEs) over a physical domain in the framework of Isogeometric analysis. For instance, we analyze the property of approximation of these spline spaces for the L 2-norm; we show that the optimal approximation order and numerical convergence rates are reached by setting a proper parameterization, although the fact that the basis functions are singular at extraordinary vertices.

We study the static and dynamical behavior of the contact line between two fluids and a solid plate by means of the Lattice Boltzmann method (LBM). The different fluid phases and their contact with the plate are simulated by means of standard Shan-Chen models. We investigate different regimes and compare the multicomponent vs. the multiphase LBM models near the contact line. A static interface profile is attained with the multiphase model just by balancing the hydrostatic pressure (due to gravity) with a pressure jump at the bottom. In order to study the same problem with the multicomponent case we propose and validate an idea of a body force acting only on one of the two fluid components. In order to reproduce results matching an infinite bath, boundary conditions at the bath side play a key role. We quantitatively compare open and wall boundary conditions and study their influence on the shape of the meniscus against static and lubrication theory solution.

In this paper we present a 2D/3D high order accurate finite volume scheme in the context of direct Arbitrary-Lagrangian-Eulerian algorithms for general hyperbolic systems of partial differential equations with non-conservative products and stiff source terms. This scheme is constructed with a single stencil polynomial reconstruction operator, a one-step space-time ADER integration which is suitably designed for dealing even with stiff sources, a nodal solver with relaxation to determine the mesh motion, a path-conservative integration technique for the treatment of non-conservative products and an a posteriori stabilization procedure derived from the so-called Multidimensional Optimal Order Detection (MOOD) paradigm. In this work we consider the seven equation Baer-Nunziato model of compressible multi-phase flows as a representative model involving non-conservative products as well as relaxation source terms which are allowed to become stiff. The new scheme is validated against a set of test cases on 2D/3D unstructured moving meshes on parallel machines and the high order of accuracy achieved by the method is demonstrated by performing a numerical convergence study. Classical Riemann problems and explosion problems with exact solutions are simulated in 2D and 3D. The overall numerical code is also profiled to provide an estimate of the computational cost required by each component of the whole algorithm.