An adaptive moving mesh finite difference method is presented to solve two types of equations with dynamic capillary pressure effect in porous media. One is the non-equilibrium Richards Equation and the other is the modified Buckley-Leverett equation. The governing equations are discretized with an adaptive moving mesh finite difference method in the space direction and an implicit-explicit method in the time direction. In order to obtain high quality meshes, an adaptive monitor function with directional control is applied to redistribute the mesh grid in every time step, then a diffusive mechanism is used to smooth the monitor function. The behaviors of the central difference flux, the standard local Lax-Friedrich flux and the local Lax-Friedrich flux with reconstruction are investigated by solving a 1D modified Buckley-Leverett equation. With the moving mesh technique, good mesh quality and high numerical accuracy are obtained. A collection of one-dimensional and two-dimensional numerical experiments is presented to demonstrate the accuracy and effectiveness of the proposed method.

In this paper, a reduced morphological transformation model with spatially dependent composition and elastic modulus is considered. The parareal in time al-gorithm introduced by Lions et al. is developed for longer-time simulation. The fine solver is based on a second-order scheme in reciprocal space, and the coarse solver is based on a multi-model backward Euler scheme, which is fast and less expensive. Numerical simulations concerning the composition with a random noise and a discontinuous curve are performed. Some microstructure characteristics at very low temperature are obtained by a variable temperature technique.

We present a study on human mobility at small spatial scales. Differently from large scale mobility, recently studied through dollar-bill tracking and mobile phone data sets within one big country or continent, we report Brownian features of human mobility at smaller scales. In particular, the scaling exponents found at the smallest scales is typically close to one-half, differently from the larger values for the exponent characterizing mobility at larger scales. We carefully analyze 12-month data of the Eduroam database within the Portuguese university of Minho. A full procedure is introduced with the aim of properly characterizing the human mobility within the network of access points composing the wireless system of the university. In particular, measures of flux are introduced for estimating a distance between access points. This distance is typically non-Euclidean, since the spatial constraints at such small scales distort the continuum space on which human mobility occurs. Since two different exponents are found depending on the scale human motion takes place, we raise the question at which scale the transition from Brownian to non-Brownian motion takes place. In this context, we discuss how the numerical approach can be extended to larger scales, using the full Eduroam in Europe and in Asia, for uncovering the transition between both dynamical regimes.

In this paper, a new numerical scheme for the time dependent Ginzburg-Landau (GL) equations under the Lorentz gauge is proposed. We first rewrite the original GL equations into a new mixed formulation, which consists of three parabolic equations for the order parameter ψ, the magnetic field σ=curlA, the electric potential θ=divA and a vector ordinary differential equation for the magnetic potential A, respectively. Then, an efficient fully linearized backward Euler finite element method (FEM) is proposed for the mixed GL system, where conventional Lagrange element method is used in spatial discretization. The new approach offers many advantages on both accuracy and efficiency over existing methods for the GL equations under the Lorentz gauge. Three physical variables ψ, σ and θ can be solved accurately and directly. More importantly, the new approach is well suitable for non-convex superconductors. We present a set of numerical examples to confirm these advantages.

A new solution methodology is proposed for solving efficiently Helmholtz problems. The proposed method falls in the category of the discontinuous Galerkin methods. However, unlike the existing solution methodologies, this method requires solving (a) well-posed local problems to determine the primal variable, and (b) a global positive semi-definite Hermitian system to evaluate the Lagrange multiplier needed to restore the continuity across the element edges. Illustrative numerical results obtained for two-dimensional interior Helmholtz problems are presented to assess the accuracy and the stability of the proposed solution methodology.

A multi-hierarchy simulation model aiming magnetic reconnection studies is developed and improved in which macroscopic and microscopic physics are computed consistently and simultaneously. Macroscopic physics is solved by mag-netohydrodynamics (MHD) algorithm, while microscopic dynamics is expressed by particle-in-cell (PIC) algorithm. The multi-hierarchy model relies on the domain decomposition method, and macro- and micro-hierarchies are interlocked smoothly by hand-shake scheme. As examination, plasma flow injection is simulated in the multi-hierarchy model. It is observed that plasmas flow from a macro-hierarchy to a micro-hierarchy across the magnetic field smoothly and continuously.

This study shows a new way to implement terrain-following σ-coordinate in a numerical model, which does not lead to the well-known “pressure gradient force (PGF)” problem. First, the causes of the PGF problem are analyzed with existing methods that are categorized into two different types based on the causes. Then, the new method that bypasses the PGF problem all together is proposed. By comparing these three methods and analyzing the expression of the scalar gradient in a curvilinear coordinate system, this study finds out that only when using the covariant scalar equations of σ-coordinate will the PGF computational form have one term in each momentum component equation, thereby avoiding the PGF problem completely. A convenient way of implementing the covariant scalar equations of σ-coordinate in a numerical atmospheric model is illustrated, which is to set corresponding parameters in the scalar equations of the Cartesian coordinate. Finally, two idealized experiments manifest that the PGF calculated with the new method is more accurate than using the classic one. This method can be used for oceanic models as well, and needs to be tested in both the atmospheric and oceanic models.

The classical discrete element approach (DEM) based on Newtonian dynamics can be divided into two major groups, event-driven methods (EDM) and time-driven methods (TDM). Generally speaking, TDM simulations are suited for cases with high volume fractions where there are collisions between multiple objects. EDM simulations are suited for cases with low volume fractions from the viewpoint of CPU time. A method combining EDM and TDM called Hybrid Algorithm of event-driven and time-driven methods (HAET) is presented in this paper. The HAET method employs TDM for the areas with high volume fractions and EDM for the remaining areas with low volume fractions. It can decrease the CPU time for simulating granular flows with strongly non-uniform volume fractions. In addition, a modified EDM algorithm using a constant time as the lower time step limit is presented. Finally, an example is presented to demonstrate the hybrid algorithm.

In this article, we discuss a least-squares/fictitious domain method for the solution of linear elliptic boundary value problems with Robin boundary conditions. Let Ω and ω be two bounded domains of Rd such that ω̅⊂Ω. For a linear elliptic problem in Ω\ω̅ with Robin boundary condition on the boundary ϒ of ω, our goal here is to develop a fictitious domain method where one solves a variant of the original problem on the full Ω, followed by a well-chosen correction over ω. This method is of the virtual control type and relies on a least-squares formulation making the problem solvable by a conjugate gradient algorithm operating in a well chosen control space. Numerical results obtained when applying our method to the solution of two-dimensional elliptic and parabolic problems are given; they suggest optimal order of convergence.

This is a brief review of the computational modeling of protein-ligand interactions using a recently developed fully polarizable continuum model (FPCM) and rational drug design. Computational modeling has become a powerful tool in understanding detailed protein-ligand interactions at molecular level and in rational drug design. To study the binding of a protein with multiple molecular species of a ligand, one must accurately determine both the relative free energies of all of the molecular species in solution and the corresponding microscopic binding free energies for all of the molecular species binding with the protein. In this paper, we aim to provide a brief overview of the recent development in computational modeling of the solvent effects on the detailed protein-ligand interactions involving multiple molecular species of a ligand related to rational drug design. In particular, we first briefly discuss the main challenges in computational modeling of the detailed protein-ligand interactions involving the multiple molecular species and then focus on the FPCM model and its applications. The FPCM method allows accurate determination of the solvent effects in the first-principles quantum mechanism (QM) calculations on molecules in solution. The combined use of the FPCM-based QM calculations and other computational modeling and simulations enables us to accurately account for a protein binding with multiple molecular species of a ligand in solution. Based on the computational modeling of the detailed protein-ligand interactions, possible new drugs may be designed rationally as either small-molecule ligands of the protein or engineered proteins that bind/metabolize the ligand. The computational drug design has successfully led to discovery and development of promising drugs.

Numerical atomic orbitals have been successfully used in molecular simulations as a basis set, which provides a nature, physical description of the electronic states and is suitable for 𝒪(N) calculations based on the strictly localized property. This paper presents a numerical analysis for some simplified atomic orbitals, with polynomial-type and confined Hydrogen-like radial basis functions respectively. We give some a priori error estimates to understand why numerical atomic orbitals are computationally efficient in electronic structure calculations.

In this study long bubble rising in a narrow channel was investigated using multiphase lattice Boltzmann method. The problem is known as a Bretherton or Taylor bubble flow [2] and is used here to verify the performance of the scheme proposed by [13]. The scheme is modified by incorporation of multiple relaxation time (MRT) collision scheme according to the original suggestion of the author. The purpose is to improve the stability of the method. The numerical simulation results show a good agreement with analytic solution provided by [2]. Moreover the convergence study demonstrates that the method achieves more than the first order of convergence. The paper investigates also the influence of simulation parameters on the interface resolution and shape.

In this paper, we study the effects of inserted needle on the subcutaneous interstitial flow. A goal is to describe the physical stress affecting cells during acupuncture treatment. The model consists of the convective Brinkman equations to describe the flow through a fibrous medium. Numerical studies in FreeFem++ are performed to illustrate the acute physical stress developed by the implantation of a needle that triggers the physiological reactions of acupuncture. We emphasize the importance of numerical experiments for advancing in modeling in acupuncture.

In this work, we develop a minimum action method (MAM) with optimal linear time scaling, called tMAM for short. The main idea is to relax the integration time as a functional of the transition path through optimal linear time scaling such that a direct optimization of the integration time is not required. The Feidlin-Wentzell action functional is discretized by finite elements, based on which h-type adaptivity is introduced to tMAM. The adaptive tMAM does not require reparametrization for the transition path. It can be applied to deal with quasi-potential: 1) When the minimal action path is subject to an infinite integration time due to critical points, tMAM with a uniform mesh converges algebraically at a lower rate than the optimal one. However, the adaptive tMAM can recover the optimal convergence rate. 2) When the minimal action path is subject to a finite integration time, tMAM with a uniform mesh converges at the optimal rate since the problem is not singular, and the optimal integration time can be obtained directly from the minimal action path. Numerical experiments have been implemented for both SODE and SPDE examples.

Dislocations are line defects in crystalline materials. The Peierls-Nabarro models are hybrid models that incorporate atomic structure of dislocation core into continuum framework. In this paper, we present a numerical method for a generalized Peierls-Nabarro model for curved dislocations, based on the fast multipole method and the iterative grid redistribution. The fast multipole method enables the calculation of the long-range elastic interaction within operations that scale linearly with the total number of grid points. The iterative grid redistribution places more mesh nodes in the regions around the dislocations than in the rest of the domain, thus increases the accuracy and efficiency. This numerical scheme improves the available numerical methods in the literature in which the long-range elastic interactions are calculated directly from summations in the physical domains; and is more flexible to handle problems with general boundary conditions compared with the previous FFT based method which applies only under periodic boundary conditions. Numerical examples using this method on the core structures of dislocations in Al and Cu and in epitaxial thin films are presented.

Plasma waves with frequencies close to the particular gyrofrequencies of the charged particles in the plasma lose energy due to cyclotron damping. We briefly discuss the gyro-resonance of low frequency plasma waves and ions particularly with regard to particle-in-cell (PiC) simulations. A setup is outlined which uses artificially excited waves in the damped regime of the wave mode's dispersion relation to track the damping of the wave's electromagnetic fields. Extracting the damping rate directly fromthe field data in real or Fourier space is an intricate and non-trivial task. We therefore present a simple method of obtaining the damping rate Γ from the simulation data. This method is described in detail, focusing on a step-by-step explanation of the course of actions. In a first application to a test simulation we find that the damping rates obtained from this simulation generally are in good agreement with theoretical predictions. We then compare the results of one-, two- and three-dimensional simulation setups and simulations with different physical parameter sets.

A unified process for the construction of hierarchical conforming bases on a range of element types is proposed based on an ab initio preservation of the underlying cohomology. This process supports not only the most common simplicial element types, as are now well known, but is generalized to squares, hexahedra, prisms and importantly pyramids. Whilst these latter cases have received (to varying degrees) attention in the literature, their foundation is less well developed than for the simplicial case. The generalization discussed in this paper is effected by recourse to basic ideas from algebraic topology (differential forms, homology, cohomology, etc) and as such extends the fundamental theoretical framework established by the work of Hiptmair and Arnold et al. for simplices. The process of forming hierarchical bases involves a recursive orthogonalization and it is shown that the resulting finite element mass, quasi-stiffness and composite matrices exhibit exponential or better growth in condition number.

A finite difference method which is second-order accurate in time and in space is proposed for two-dimensional fractional percolation equations. Using the Fourier transform, a general approximation for the mixed fractional derivatives is analyzed. An approach based on the classical Crank-Nicolson scheme combined with the Richardson extrapolation is used to obtain temporally and spatially second-order accurate numerical estimates. Consistency, stability and convergence of the method are established. Numerical experiments illustrating the effectiveness of the theoretical analysis are provided.

This paper presents a numerical and experimental study on hydrodynamic behavior of thin liquid films in rectangular domains. Three-dimensional computer simulations were performed using the lattice Boltzmann equation method (LBM). The liquid films laying on solid and liquid substrates are considered. The rupture of liquid films in computations is initiated via the thermocapillary (Marangoni) effect by applying an initial spatially localized temperature perturbation. The rupture scenario is found to depend on the shape of the temperature distribution and on the wettability of the solid substrate. For a wettable solid substrate, complete rupture does not occur: a residual thin liquid film remains at the substrate in the region of pseudo-rupture. For a non-wettable solid substrate, a sharp-peaked axisymmetric temperature distribution induces the rupture at the center of symmetry where the temperature is maximal. Axisymmetric temperature distribution with a flat-peaked temperature profile initiates rupture of the liquid film along a circle at some distance from the center of symmetry. The outer boundary of the rupture expands, while the inner liquid disk transforms into a toroidal figure and ultimately into an oscillating droplet.

We also apply the LBM to simulations of an evolution of one or two holes in liquid films for two-layer systems of immiscible fluids in a rectangular cell. The computed patterns are successfully compared against the results of experimental visualizations. Both the experiments and the simulations demonstrate that the initially circular holes evolved in the rectangular cell undergoing drastic changes of their shape under the effects of the surface tension and gravity. In the case of two interacting holes, the disruption of the liquid bridge separating two holes is experimentally observed and numerically simulated.

The lattice Boltzmann method is applied to the investigations of the diffusivity and the permeability in the gas diffusion layer (GDL) of the polymer electrolyte fuel cell (PEFC). The effects of the configuration of water droplets, the porosity of the GDL, the viscosity ratio of water to air, and the surface wettability of the GDL are investigated. From the simulations under the PEFC operating conditions, it is found that the heterogeneous water network and the high porosity improve the diffusivity and the permeability, and the hydrophobic surface decreases the permeability.