In this paper we consider (hierarchical, Lagrange) reduced basis approximation and a posteriori error estimation for potential flows in affinely parametrized geometries. We review the essential ingredients: i) a Galerkin projection onto a low-dimensional space associated with a smooth "parametric manifold" in order to get a dimension reduction; ii) an efficient and effective greedy sampling method for identification of optimal and numerically stable approximations to have a rapid convergence; iii) an a posteriori error estimation procedure: rigorous and sharp bounds for the linear-functional outputs of interest and over the potential solution or related quantities of interest like velocity and/or pressure; iv) an Offline-Online computational decomposition strategies to achieve a minimum marginal computational cost for high performance in the real-time and many-query (e.g., design and optimization) contexts. We present three illustrative results for inviscid potential flows in parametrized geometries representing a Venturi channel, a circular bend and an added mass problem.

We report kinetic Monte-Karlo (KMC) simulation of self-assembled synthesis of nanocrystals by physical vapor deposition (PVD), which is one of the most flexible, efficient, and clean techniques to fabricate nanopatterns. In particular, self-assembled arrays of nanocrystals can be synthesized by PVD. However size, shape and density of self-assembled nanocrystals are highly sensitive to the process conditions such as duration of deposition, temperature, substrate material, etc. To efficiently synthesize nanocrystalline arrays by PVD, the process control factors should be understood in detail. KMC simulations of film deposition are an important tool for understanding the mechanisms of film deposition. In this paper, we report a KMC modeling that explicitly represents PVD synthesis of self-assembled nanocrystals. We study how varying critical process parameters such as deposition rate, duration, temperature, and substrate type affect the lateral 2D morphologies of self-assembled metallic islands on substrates, and compare our results with experimentally observed surface morphologies generated by PVD. Our simulations align well with experimental results reported in the literature.

An anisotropic solution adaptive method based on unstructured quadrilateral meshes for inviscid compressible flows is proposed. The data structure, the directional refinement and coarsening, including the method for initializing the refined new cells, for the anisotropic adaptive method are described. It provides efficient high resolution of flow features, which are aligned with the original quadrilateral mesh structures. Five different cases are provided to show that it could be used to resolve the anisotropic flow features and be applied to model the complex geometry as well as to keep a relative high order of accuracy on an efficient anisotropic mesh.

We present an algorithm for the stochastic simulation of gene expression and heterogeneous population dynamics. The algorithm combines an exact method to simulate molecular-level fluctuations in single cells and a constant-number Monte Carlo method to simulate time-dependent statistical characteristics of growing cell populations. To benchmark performance, we compare simulation results with steady-state and time-dependent analytical solutions for several scenarios, including steady-state and time-dependent gene expression, and the effects on population heterogeneity of cell growth, division, and DNA replication. This comparison demonstrates that the algorithm provides an efficient and accurate approach to simulate how complex biological features influence gene expression. We also use the algorithm to model gene expression dynamics within "bet-hedging" cell populations during their adaption to environmental stress. These simulations indicate that the algorithm provides a framework suitable for simulating and analyzing realistic models of heterogeneous population dynamics combining molecular-level stochastic reaction kinetics, relevant physiological details and phenotypic variability.

In a two-dimensional (2D) photonic crystal (PhC) composed of circular cylinders (dielectric rods or air holes) on a square or triangular lattice, various PhC devices can be created by removing or modifying some cylinders. Most existing numerical methods for PhC devices give rise to large sparse or smaller but dense linear systems, all of which are expensive to solve if the device is large. In a previous work [Z. Hu et al., Optics Express, 16 (2008), 17383-17399], an efficient Dirichlet-to-Neumann (DtN) map method was developed for general 2D PhC devices with an infinite background PhC to take full advantage of the underlying lattice structure. The DtN map of a unit cell is an operator that maps the wave field to its normal derivative on the cell boundary and it allows one to avoid computing the wave field in the interior of the unit cell. In this paper, we extend the DtN map method to PhC devices with a finite background PhC. Since there is no bandgap effect to confine the light in a finite PhC, a different technique for truncating the domain is needed. We enclose the finite structure with a layer of empty boundary and corner unit cells, and approximate the DtN maps of these cells based on expanding the scattered wave in outgoing plane waves. Our method gives rise to a relatively small and sparse linear systems that are particularly easy to solve.

Thermochronometer data offer a powerful tool for quantifying a wide range of geologic processes, such as the deformation and erosion of mountain ranges, topographic evolution, and hydrocarbon maturation. With increasing interest to quantify a wider range of complicated geologic processes, more sophisticated techniques are needed. This paper is concerned with an inverse problem method for interpreting the thermochronometer data quantitatively. Two novel models are proposed to simulate the crustal thermal fields and paleo mountain topography as a function of tectonic and surface processes. One is a heat transport model that describes the change of temperature of rocks; while the other is surface process model which explains the change of mountain topography. New computational algorithms are presented for solving the inverse problem of the coupled system of these two models. The model successfully provides a new tool for reconstructing the kinematic and the topographic history of mountains.

We derive a perfectly matched layer (PML) for the Schrödinger equation using a modal ansatz. We derive approximate error formulas for the modeling error from the outer boundary of the PML and the error from the discretization in the layer and show how to choose layer parameters so that these errors are matched and optimal performance of the PML is obtained. Numerical computations in 1D and 2D demonstrate that the optimized PML works efficiently at a prescribed accuracy for the zero potential case, with a layer of width less than a third of the de Broglie wavelength corresponding to the dominating frequency.

A numerical procedure for the evaluation of equivalent permeability tensor for fractured vuggy porous media is presented. At first we proposed a new conceptual model, i.e., discrete fracture-vug network model, to model the realistic fluid flow in fractured vuggy porous medium on fine scale. This new model consists of three systems: rock matrix system, fractures system, and vugs system. The fractures and vugs are embedded in porous rock, and the isolated vugs could be connected via discrete fracture network. The flow in porous rock and fractures follows Darcy's law, and the vugs system is free fluid region. Based on two-scale homogenization theory, we obtained an equivalent macroscopic Darcy's law on coarse scale from fine-scale discrete fracture-vug network model. A finite element numerical formulation for homogenization equations is developed. The method is verified through application to a periodic model problem and then is applied to the calculation of equivalent permeability tensor of porous media with complex fracture-vug networks. The applicability and validity of the method for these more general fractured vuggy systems are assessed through a simple test of the coarse-scale model.

In this paper, a new sharp-interface approach to simulate compressible multiphase flows is proposed. The new scheme consists of a high order WENO finite volume scheme for solving the Euler equations coupled with a high order path-conservative discontinuous Galerkin finite element scheme to evolve an indicator function that tracks the material interface. At the interface our method applies ghost cells to compute the numerical flux, as the ghost fluid method. However, unlike the original ghost fluid scheme of Fedkiw et al. [15], the state of the ghost fluid is derived from an approximate-state Riemann solver, similar to the approach proposed in [25], but based on a much simpler formulation. Our formulation leads only to one single scalar nonlinear algebraic equation that has to be solved at the interface, instead of the system used in [25]. Away from the interface, we use the new general Osher-type flux recently proposed by Dumbser and Toro [13], which is a simple but complete Riemann solver, applicable to general hyperbolic conservation laws. The time integration is performed using a fully-discrete one-step scheme, based on the approaches recently proposed in [5, 7]. This allows us to evolve the system also with time-accurate local time stepping. Due to the sub-cell resolution and the subsequent more restrictive time-step constraint of the DG scheme, a local evolution for the indicator function is applied, which is matched with the finite volume scheme for the solution of the Euler equations that runs with a larger time step. The use of a locally optimal time step avoids the introduction of excessive numerical diffusion in the finite volume scheme. Two different fluids have been used, namely an ideal gas and a weakly compressible fluid modeled by the Tait equation. Several tests have been computed to assess the accuracy and the performance of the new high order scheme. A verification of our algorithm has been carefully carried out using exact solutions as well as a comparison with other numerical reference solutions. The material interface is resolved sharply and accurately without spurious oscillations in the pressure field.