Plasmas in modern tokamak experiments contain a significant fraction of impurity ion species in addition to main deuterium background. A new unlike-particle collision operator for δf particle simulation has been developed to study the nonlocal effects of impurities due to finite ion orbits on neoclassical transport in toroidal plasmas. A new algorithm for simulation of cross-collisions between different ion species includes test-particle and conserving field-particle operators. An improved field-particle operator is designed to exactly enforce conservation of number, momentum and energy.

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.

The properties of hydrogen atoms in a nano-diamond grain surrounded by an amorphous carbon shell are studied with Tight Binding computer simulations. Our samples model nano-diamond grains, of a few nanometers in size, that nucleate within an amorphous carbon matrix, as observed in deposition from a hydrocarbon rich plasma. The calculations show that the average hydrogen interstitial formation energy in the amorphous region is lower than in the nano-diamond core, therefore hydrogen interstitial sites in the in the amorphous region are more stable than in the nano-diamond core. This formation energy difference is the driving force for the diffusion of hydrogen atoms from nano-diamond grains into amorphous carbon regions. An energy well was observed on the amorphous side of the nano-diamond amorphous carbon interface: hydrogen atoms are expected to be trapped here. This scenario agrees with experimental results which show that hydrogen retention of diamond films increases with decreasing grain size, and suggest that hydrogen is bonded and trapped in nano-diamond grain boundaries and on internal grain surfaces.

This article is a brief survey of David Gottlieb’s extraordinary research career. It is impossible to give a thorough presentation of all his research and the impact of his work, but we shall describe the main contributions and give examples of the results in some of his papers. David was for many years the dominating person in the development of spectral methods, and we devote much of the space in this article to this field.

Given a piecewise smooth function, it is possible to construct a global expansion in some complete orthogonal basis, such as the Fourier basis. However, the local discontinuities of the function will destroy the convergence of global approximations, even in regions for which the underlying function is analytic. The global expansions are contaminated by the presence of a local discontinuity, and the result is that the partial sums are oscillatory and feature non-uniform convergence. This characteristic behavior is called the Gibbs phenomenon. However, David Gottlieb and Chi-Wang Shu showed that these slowly and non-uniformly convergent global approximations retain within them high order information which can be recovered with suitable postprocessing. In this paper we review the history of the Gibbs phenomenon and the story of its resolution.

Variational image segmentation based on the Mumford and Shah model [31], together with implementation by the piecewise constant level-set method (PCLSM) [26], leads to fully nonlinear Total Variation (TV)-Allen-Cahn equations. The commonly-used numerical approaches usually suffer from the difficulties not only with the non-differentiability of the TV-term, but also with directly evolving the discontinuous piecewise constant-structured solutions. In this paper, we propose efficient dual algorithms to overcome these drawbacks. The use of a splitting-penalty method results in TV-Allen-Cahn type models associated with different “double-well” potentials, which allow for the implementation of the dual algorithm of Chambolle [8]. Moreover, we present a new dual algorithm based on an edge-featured penalty of the dual variable, which only requires to solve a vectorial Allen-Cahn type equation with linear ∇(div)-diffusion rather than fully nonlinear diffusion in the Chambolle’s approach. Consequently, more efficient numerical algorithms such as time-splitting method and Fast Fourier Transform (FFT) can be implemented. Various numerical tests show that two dual algorithms are much faster and more stable than the primal gradient descent approach, and the new dual algorithm is at least as efficient as the Chambolle’s algorithm but is more accurate. We demonstrate that the new method also provides a viable alternative for image restoration.

We show that an enslaved phase-separation front moving with diffusive speeds can leave alternating domains of increasing size in their wake. We find the size and spacing of these domains is identical to Liesegang patterns. For equal composition of the components we are able to predict the exact form of the pattern analytically. To our knowledge this is the first fully analytical derivation of the Liesegang laws. We also show that there is a critical value for C below which only two domains are formed. Our analytical predictions are verified by numerical simulations using a lattice Boltzmann method.

A discontinuous Galerkin method for the ideal 5 moment two-fluid plasma system is presented. The method uses a second or third order discontinuous Galerkin spatial discretization and a third order TVD Runge-Kutta time stepping scheme. The method is benchmarked against an analytic solution of a dispersive electron acoustic square pulse as well as the two-fluid electromagnetic shock [1] and existing numerical solutions to the GEM challenge magnetic reconnection problem [2]. The algorithm can be generalized to arbitrary geometries and three dimensions. An approach to maintaining small gauge errors based on error propagation is suggested.

We report kinetic Monte-Karlo (KMC) simulation of self-assembled synthesis of nanocrystals by physical vapor deposition (PVD), which is one of 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.

The dynamic behaviors of continuous and discrete flows in superhydrophobic microchannels are investigated with a lattice Boltzmann model. Typical characters of the superhydrophobic phenomenon are well observed from our simulations, including air trapped in the surface microstructures, high contact angles, low contact angle hysteresis, and reduced friction to fluid motions. Increasing the roughness of a hydrophobic surface can produce a large flow rate through the channel due to the trapped air, implying less friction or large apparent slip. The apparent slip length appears to be independent to the channel width and could be considered as a surface property. For a moving droplet, its behavior is affected by the surface roughness from two aspects: the contact angle difference between its two ends and the surface-liquid interfacial friction. As a consequence, the resulting droplet velocity changes with the surface roughness as firstly decreasing and then increasing. Simulation results are also compared with experimental observations and better agreement has been obtained than that from other numerical method. The information from this study could be valuable for microfluidic systems.

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.

The simulation of multiphase flows is an outstanding challenge, due to the inherent complexity of the underlying physical phenomena and to the fact that multiphase flows are very diverse in nature, and so are the laws governing their dynamics. In the last two decades, a new class of mesoscopic methods, based on minimal lattice formulation of Boltzmann kinetic equation, has gained significant interest as an efficient alternative to continuum methods based on the discretisation of the NS equations for non ideal fluids. In this paper, three different multiphase models based on the lattice Boltzmann method (LBM) are discussed, in order to assess the capability of the method to deal with multiphase flows on a wide spectrum of operating conditions and multiphase phenomena. In particular, the range of application of each method is highlighted and its effectiveness is qualitatively assessed through comparison with numerical and experimental literature data.

Detecting corrosion by electrical field can be modeled by a Cauchy problem of Laplace equation in annulus domain under the assumption that the thickness of the pipe is relatively small compared with the radius of the pipe. The interior surface of the pipe is inaccessible and the nondestructive detection is solely based on measurements from the outer layer. The Cauchy problem for an elliptic equation is a typical ill-posed problem whose solution does not depend continuously on the boundary data. In this work, we assume that the measurements are available on the whole outer boundary on an annulus domain. By imposing reasonable assumptions, the theoretical goal here is to derive the stabilities of the Cauchy solutions and an energy regularization method. Relationship between the proposed energy regularization method and the Tikhonov regularization with Morozov principle is also given. A novel numerical algorithm is proposed and numerical examples are given.

In many problems, one wishes to solve the Helmholtz equation with variable coefficients within the Laplacian-like term and use a high order accurate method (e.g., fourth order accurate) to alleviate the points-per-wavelength constraint by reducing the dispersion errors. The variation of coefficients in the equation may be due to an inhomogeneous medium and/or non-Cartesian coordinates. This renders existing fourth order finite difference methods inapplicable. We develop a new compact scheme that is provably fourth order accurate even for these problems. We present numerical results that corroborate the fourth order convergence rate for several model problems.

This paper presents an exponential compact higher order scheme for Convection-Diffusion Equations (CDE) with variable and nonlinear convection coefficients. The scheme is for one-dimensional problems and produces a tri-diagonal system of equations which can be solved efficiently using Thomas algorithm. For two-dimensional problems, the scheme produces an accuracy over a compact nine point stencil which can be solved using any line iterative approach with alternate direction implicit procedure. The convergence of the iterative procedure is guaranteed as the coefficient matrix of the developed scheme satisfies the conditions required to be positive. Wave number analysis has been carried out to establish that the scheme is comparable in accuracy with spectral methods. The higher order accuracy and better rate of convergence of the developed scheme have been demonstrated by solving numerous model problems for one and two-dimensional CDE, where the solutions have the sharp gradient at the solution boundary.

The stochastic collocation method using sparse grids has become a popular choice for performing stochastic computations in high dimensional (random) parameter space. In addition to providing highly accurate stochastic solutions, the sparse grid collocation results naturally contain sensitivity information with respect to the input random parameters. In this paper, we use the sparse grid interpolation and cubature methods of Smolyak together with combinatorial analysis to give a computationally efficient method for computing the global sensitivity values of Sobol’. This method allows for approximation of all main effect and total effect values from evaluation of f on a single set of sparse grids. We discuss convergence of this method, apply it to several test cases and compare to existing methods. As a result which may be of independent interest, we recover an explicit formula for evaluating a Lagrange basis interpolating polynomial associated with the Chebyshev extrema. This allows one to manipulate the sparse grid collocation results in a highly efficient manner.

A robust and efficient solver coupling computational fluid dynamics (CFD) with discrete element method (DEM) is developed to simulate particle-laden flows in various physical settings. An interpolation algorithm suitable for unstructured meshes is proposed to translate between mesh-based Eulerian fields and particle-based La-grangian quantities. The interpolation scheme reduces the mesh-dependence of the averaging and interpolation procedures. In addition, the fluid-particle interaction terms are treated semi-implicitly in this algorithm to improve stability and to maintain accuracy. Finally, it is demonstrated that sub-stepping is desirable for fluid-particle systems with small Stokes numbers. A momentum-conserving sub-stepping technique is introduced into the fluid-particle coupling procedure, so that problems with a wide range of time scales can be solved without resorting to excessively small time steps in the CFD solver. Several numerical examples are presented to demonstrate the capabilities of the solver and the merits of the algorithm.

This work proposes an extension to Boltzmann BGK equation for dense gases. The present model has an H-theorem and it allows choice of the Prandtl number as an independent parameter. I show that similar to Enskog equation this equation can reproduce dynamics of dense gases.

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.