As the numerical resolution is increased and the discretisation error decreases, the lattice Boltzmann method tends towards the discrete-velocity Boltzmann equation (DVBE). An expression for the propagation properties of plane sound waves is found for this equation. This expression is compared to similar ones from the Navier-Stokes and Burnett models, and is found to be closest to the latter. The anisotropy of sound propagation with the DVBE is examined using a two-dimensional velocity set. It is found that both the anisotropy and the deviation between the models is negligible if the Knudsen number is less than 1 by at least an order of magnitude.

The implicit 2D3V particle-in-cell (PIC) code developed to study the interaction of ultrashort pulse lasers with matter [G. M. Petrov and J. Davis, Computer Phys. Comm. 179, 868 (2008); Phys. Plasmas 18, 073102 (2011)] has been parallelized using MPI (Message Passing Interface). The parallelization strategy is optimized for a small number of computer cores, up to about 64. Details on the algorithm implementation are given with emphasis on code optimization by overlapping computations with communications. Performance evaluation for 1D domain decomposition has been made on a small Linux cluster with 64 computer cores for two typical regimes of PIC operation: “particle dominated”, for which the bulk of the computation time is spent on pushing particles, and “field dominated”, for which computing the fields is prevalent. For a small number of computer cores, less than 32, the MPI implementation offers a significant numerical speed-up. In the “particle dominated” regime it is close to the maximum theoretical one, while in the “field dominated” regime it is about 75-80 % of the maximum speed-up. For a number of cores exceeding 32, performance degradation takes place as a result of the adopted 1D domain decomposition. The code parallelization will allow future implementation of atomic physics and extension to three dimensions.

In this paper, a novel second-order two-scale (SOTS) computational method is developed for nonlinear dynamic thermo-mechanical problems of composites with cylindrical periodicity. The non-linearities of these multi-scale problems were caused by the temperature-dependent properties of the composites. Firstly, the formal SOTS solutions for these problems are constructed by the multiscale asymptotic analysis. Then we theoretically explain the importance of the SOTS solutions by the error analysis in the pointwise sense. In addition, a SOTS numerical algorithm is proposed in detail to effectively solve these problems. Finally, some numerical examples verify the feasibility and effectiveness of the SOTS numerical algorithm we proposed.

The emission of scission neutrons from fissioning nuclei is of high practical interest. To study this process we have used the sudden approximation and also a more realistic approach that takes into account the scission dynamics. Numerically, this implies the solution of the bi-dimensional Schrödinger equation, both stationary and time-dependent. To describe axially symmetric extremely deformed nuclear shapes, we have used the Cassini parametrization. The Hamiltonian is discretized by using finite difference approximations of the derivatives. The main computational challenges are the solution of algebraic eigenvalue problems and of linear systems with large sparse matrices. We have employed appropriate procedures (Arnoldi and bi-conjugate gradients). The numerical solutions have been used to evaluate physical quantities, like the number of emitted neutrons per scission event, the primary fragments’ excitation energy and the distribution of the emission points.

We present a high precision frequency determination method for digitized NMR FID signals. The method employs high precision numerical integration rather than simple summation as in many other techniques. With no independent knowledge of the other parameters of a NMR FID signal (phase ф, amplitude A, and transverse relaxation time T2) this method can determine the signal frequency f0 with a precision of if the observation time T ≫ T2. The method is especially convenient when the detailed shape of the observed FT NMR spectrum is not well defined. When T2 is +∞ and the signal becomes pure sinusoidal, the precision of the method is which is one order more precise than the ±1 count error induced precision of a typical frequency counter. Analysis of this method shows that the integration reduces the noise by bandwidth narrowing as in a lock-in amplifier, and no extra signal filters are needed. For a pure sinusoidal signal we find from numerical simulations that the noise-induced error in this method reaches the Cramer-Rao Lower Band (CRLB) on frequency determination. For the damped sinusoidal case of most interest, the noise-induced error is found to be within a factor of 2 of CRLB when the measurement time T is 2 or 3 times larger than T2. We discuss possible improvements for the precision of this method.

We show that a single particle distribution for the “energy-conserving” D2Q13 lattice Boltzmann scheme can simulate coupled effects involving advection and diffusion of velocity and temperature. We consider various test cases: non-linear waves with periodic boundary conditions, a test case with buoyancy, propagation of transverse waves, Couette and Poiseuille flows. We test various boundary conditions and propose to mix bounce-back and anti-bounce-back numerical boundary conditions to take into account velocity and temperature Dirichlet conditions. We present also first results for the de Vahl Davis heated cavity. Our results are compared with the coupled D2Q9-D2Q5 lattice Boltzmann approach for the Boussinesq system and with an elementary finite differences solver for the compressible Navier-Stokes equations. Our main experimental result is the loss of symmetry in the de Vahl Davis cavity computed with the single D2Q13 lattice Boltzmann model without the Boussinesq hypothesis. This result is confirmed by a direct Navier Stokes simulation with finite differences.

A new set of boundary conditions has been derived by rigorous methods for the shallow water equations in a limited domain. The aim of this article is to present these boundary conditions and to report on numerical simulations which have been performed using these boundary conditions. The new boundary conditions which are mildly dissipative let the waves move freely inside and outside the domain. The problems considered include a one-dimensional shallow water system with two layers of fluids and a two-dimensional inviscid shallow water system in a rectangle.

Lattice-Boltzmann methods are versatile numerical modeling techniques capable of reproducing a wide variety of fluid-mechanical behavior. These methods are well suited to parallel implementation, particularly on the single-instruction multiple data (SIMD) parallel processing environments found in computer graphics processing units (GPUs).

Although recent programming tools dramatically improve the ease with which GPUbased applications can be written, the programming environment still lacks the flexibility available to more traditional CPU programs. In particular, it may be difficult to develop modular and extensible programs that require variable on-device functionality with current GPU architectures.

This paper describes a process of automatic code generation that overcomes these difficulties for lattice-Boltzmann simulations. It details the development of GPU-based modules for an extensible lattice-Boltzmann simulation package – LBHydra. The performance of the automatically generated code is compared to equivalent purposewritten codes for both single-phase,multiphase, andmulticomponent flows. The flexibility of the new method is demonstrated by simulating a rising, dissolving droplet moving through a porous medium with user generated lattice-Boltzmann models and subroutines.

In this paper, we study the selectivity of the potassium channel KcsA by a recently developed image-charge solvation method (ICSM) combined with molecular dynamics simulations. The hybrid solvation model in the ICSM is able to demonstrate atomistically the function of the selectivity filter of the KcsA channel when potassium and sodium ions are considered and their distributions inside the filter are simulated. Our study also shows that the reaction field effect, explicitly accounted for through image charge approximation in the ICSM model, is necessary in reproducing the correct selectivity property of the potassium channels.

We present a new splitting method for time-dependent convention-dominated diffusion problems. The original convention diffusion system is split into two sub-systems: a pure convection system and a diffusion system. At each time step, a convection problem and a diffusion problem are solved successively. A few important features of the scheme lie in the facts that the convection subproblem is solved explicitly and multistep techniques can be used to essentially enlarge the stability region so that the resulting scheme behaves like an unconditionally stable scheme; while the diffusion subproblem is always self-adjoint and coercive so that they can be solved efficiently using many existing optimal preconditioned iterative solvers. The scheme can be extended for solving the Navier-Stokes equations, where the nonlinearity is resolved by a linear explicit multistep scheme at the convection step, while only a generalized Stokes problem is needed to solve at the diffusion step and the major stiffness matrix stays invariant in the time marching process. Numerical simulations are presented to demonstrate the stability, convergence and performance of the single-step and multistep variants of the new scheme.

The Lattice Boltzmann Method (LBM) has established itself as a popular numerical method in computational fluid dynamics. Several advancements have been recently made in LBM, which include multiple-relaxation-time LBM to simulate anisotropic advection-diffusion processes. Because of the importance of LBM simulations for transport problems in subsurface and reactive flows, one needs to study the accuracy and structure preserving properties of numerical solutions under the LBM. The solutions to advective-diffusive systems are known to satisfy maximum principles, comparison principles, the non-negative constraint, and the decay property. In this paper, using several numerical experiments, it will be shown that current single- and multiple-relaxation-time lattice Boltzmann methods fail to preserve these mathematical properties for transient diffusion-type equations. We will also show that these violations may not be removed by simply refining the discretization parameters. More importantly, it will be shown that meeting stability conditions alone does not guarantee the preservation of the aforementioned mathematical principles and physical constraints in the discrete setting. A discussion on the source of these violations and possible approaches to avoid them is included. A condition to guarantee the non-negativity of concentration under LBM in the case of isotropic diffusion is also derived. The impact of this research is twofold. First, the study poses several outstanding research problems, which should guide researchers to develop LBM-based formulations for transport problems that respect important mathematical properties and physical constraints in the discrete setting. This paper can also serve as a good source of benchmark problems for such future research endeavors. Second, this study cautions the practitioners of the LBM for transport problems with the associated numerical deficiencies of the LBM, and provides guidelines for performing predictive simulations of advective-diffusive processes using the LBM.

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.

The radiative transfer equation (RTE) arises in many different areas of science and engineering. In this paper, we propose and investigate a discrete-ordinate discontinuous-streamline diffusion (DODSD) method for solving the RTE, which is a combination of the discrete-ordinate technique and the discontinuous-streamline diffusion method. Different from the discrete-ordinate discontinuous Galerkin (DODG) method for the RTE, an artificial diffusion parameter is added to the test functions in the spatial discretization. Stability and error estimates in certain norms are proved. Numerical results show that the proposed method can lead to a more accurate approximation in comparison with the DODG method.

This paper focuses on the development of an efficient, three-dimensional, thermo-mechanical, nonlinear-Stokes flow computational model for ice sheet simulation. The model is based on the parallel finite element model developed in [14] which features high-order accurate finite element discretizations on variable resolution grids. Here, we add an improved iterative solution method for treating the nonlinearity of the Stokes problem, a new high-order accurate finite element solver for the temperature equation, and a new conservative finite volume solver for handling mass conservation. The result is an accurate and efficient numerical model for thermo-mechanical glacier and ice-sheet simulations. We demonstrate the improved efficiency of the Stokes solver using the ISMIP-HOM Benchmark experiments and a realistic test case for the Greenland ice-sheet. We also apply our model to the EISMINT-II benchmark experiments and demonstrate stable thermo-mechanical ice sheet evolution on both structured and unstructured meshes. Notably, we find no evidence for the “cold spoke” instabilities observed for these same experiments when using finite difference, shallow-ice approximation models on structured grids.

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.

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.

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.

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.

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.