In this contribution, a new class of lattice Boltzmann schemes is introduced and studied. These schemes are presented in a framework that generalizes the multiple relaxation times method of d’Humières. They extend also the Geier’s cascaded method. The relaxation phase takes place in a moving frame involving a set of moments depending on a given relative velocity field. We establish with the Taylor expansion method that the equivalent partial differential equations are identical to the ones obtained with the multiple relaxation times method up to the second order accuracy. The method is then performed to derive the equivalent equations up to third order accuracy.

Experimental data shows that the binding of human prolactin (hPRL) to human prolactin receptor (hPRLr-ECD) is strongly pH-dependent, while the binding of the same receptor to human growth hormone (hGH) is pH-independent. Here we carry in silico analysis of the molecular effects causing such a difference and reveal the role of individual amino acids. It is shown that the computational modeling correctly predicts experimentally determined pKa’s of histidine residues in an unbound state in the majority of the cases and the pH-dependence of the binding free energy. Structural analysis carried in conjunction with calculated pH-dependence of the binding revealed that the main reason for pH-dependence of the binding of hPRL-hPRLr-ECD is a number of salt-bridges across the interface of the complex, while no salt-bridges are formed in the hGH-hPRlr-ECD. Specifically, most of the salt-bridges involve histidine residues and this is the reason for the pH-dependence across a physiological range of pH. The analysis not only revealed the molecular mechanism of the pH-dependence of the hPRL-hPRLr-ECD, but also provided critical insight into the underlying physic-chemical mechanism.

In this paper, a compact third-order gas-kinetic scheme is proposed for the compressible Euler and Navier-Stokes equations. The main reason for the feasibility to develop such a high-order scheme with compact stencil, which involves only neighboring cells, is due to the use of a high-order gas evolution model. Besides the evaluation of the time-dependent flux function across a cell interface, the high-order gas evolution model also provides an accurate time-dependent solution of the flow variables at a cell interface. Therefore, the current scheme not only updates the cell averaged conservative flow variables inside each control volume, but also tracks the flow variables at the cell interface at the next time level. As a result, with both cell averaged and cell interface values, the high-order reconstruction in the current scheme can be done compactly. Different from using a weak formulation for high-order accuracy in the Discontinuous Galerkin method, the current scheme is based on the strong solution, where the flow evolution starting from a piecewise discontinuous high-order initial data is precisely followed. The cell interface time-dependent flow variables can be used for the initial data reconstruction at the beginning of next time step. Even with compact stencil, the current scheme has third-order accuracy in the smooth flow regions, and has favorable shock capturing property in the discontinuous regions. It can be faithfully used from the incompressible limit to the hypersonic flow computations, and many test cases are used to validate the current scheme. In comparison with many other high-order schemes, the current method avoids the use of Gaussian points for the flux evaluation along the cell interface and the multi-stage Runge-Kutta time stepping technique. Due to its multidimensional property of including both derivatives of flow variables in the normal and tangential directions of a cell interface, the viscous flow solution, especially those with vortex structure, can be accurately captured. With the same stencil of a second order scheme, numerical tests demonstrate that the current scheme is as robust as well-developed second-order shock capturing schemes, but provides more accurate numerical solutions than the second order counterparts.

In this short note we present a derivation of the Spectral Difference Scheme from a Discontinuous Galerkin (DG) discretization of a nonlinear conservation law. This allows interpretation of the Spectral Difference Scheme as a particular discretization under the quadrature-free nodal DG paradigm. Moreover, it enables identification of the key differences between the Spectral Difference Scheme and standard nodal DG schemes.

The computation of the radiative transfer equation is expensive mainly due to two stiff terms: the transport term and the collision operator. The stiffness in the former comes from the fact that particles (such as photons) travel at the speed of light, while that in the latter is due to the strong scattering in the optically thick region. We study the fully implicit scheme for this equation to account for the stiffness. The main challenge in the implicit treatment is the coupling between the spacial and angular coordinates that requires the large size of the to-be-inverted matrix, which is also ill-conditioned and not necessarily symmetric. Our main idea is to utilize the spectral structure of the ill-conditioned matrix to construct a pre-conditioner, which, along with an exquisite split of the spatial and angular dependence, significantly improve the condition number and allows a matrix-free treatment. We also design a fast solver to compute this pre-conditioner explicitly in advance. Our method is shown to be efficient in both diffusive and free streaming limit, and the computational cost is comparable to the state-of-the-art method. Various examples including anisotropic scattering and two-dimensional problems are provided to validate the effectiveness of our method.

In this paper, a numerical method is presented for simulating the 3D interfacial flows with insoluble surfactant. The numerical scheme consists of a 3D immersed interface method (IIM) for solving Stokes equations with jumps across the interface and a 3D level-set method for solving the surfactant convection-diffusion equation along a moving and deforming interface. The 3D IIM Poisson solver modifies the one in the literature by assuming that the jump conditions of the solution and the flux are implicitly given at the grid points in a small neighborhood of the interface. This assumption is convenient in conjunction with the level-set techniques. It allows standard Lagrangian interpolation for quantities at the projection points on the interface. The interface jump relations are re-derived accordingly. A novel rotational procedure is given to generate smooth local coordinate systems and make effective interpolation. Numerical examples demonstrate that the IIM Poisson solver and the Stokes solver achieve second-order accuracy. A 3D drop with insoluble surfactant under shear flow is investigated numerically by studying the influences of different physical parameters on the drop deformation.

High fidelity modeling and simulation of moderately dense sprays at relatively low cost is still a major challenge for many applications. For that purpose, we introduce a new multi-fluid model based on a two-size moment formalism in sections, which are size intervals of discretization. It is derived from a Boltzmann type equation taking into account drag, evaporation and coalescence, which are representative of the complex terms that arise in multi-physics environments. The closure of the model comes from a reconstruction of the distribution. A piecewise affine reconstruction in size is thoroughly analyzed in terms of stability and accuracy, a key point for a high-fidelity and reliable description of the spray. Robust and accurate numerical methods are then developed, ensuring the realizability of the moments. The model and method are proven to describe the spray with a high accuracy in size and size-conditioned variables, resorting to a lower number of sections compared to one size moment methods. Moreover, robustness is ensured with efficient and tractable algorithms despite the numerous couplings and various algebra thanks to a tailored overall strategy. This strategy is successfully tested on a difficult 2D unsteady case, which proves the efficiency of the modeling and numerical choices.

The ordered patterns formed by microphase-separated block copolymer systems demonstrate periodic symmetry, and all periodic structures belong to one of 230 space groups. Based on this fact, a strategy of estimating the initial values of self-consistent field theory to discover ordered patterns of block copolymers is developed. In particular, the initial period of the computational box is estimated by the Landau-Brazovskii model as well. By planting the strategy into the whole-space discrete method, several new metastable patterns are discovered in diblock copolymers.

In multi physics computations where a compressible fluid is coupled with a linearly elastic solid, it is standard to enforce continuity of the normal velocities and of the normal stresses at the interface between the fluid and the solid. In a numerical scheme, there are many ways that velocity- and stress-continuity can be enforced in the discrete approximation. This paper performs a normal mode stability analysis of the linearized problem to investigate the stability of different numerical interface conditions for a model problem approximated by upwind type finite difference schemes. The analysis shows that depending on the ratio of densities between the solid and the fluid, some numerical interface conditions are stable up to the maximal CFL-limit, while other numerical interface conditions suffer from a severe reduction of the stable CFL-limit. The paper also presents a new interface condition, obtained as a simplified characteristic boundary condition, that is proved to not suffer from any reduction of the stable CFL-limit. Numerical experiments in one space dimension show that the new interface condition is stable also for computations with the non-linear Euler equations of compressible fluid flow coupled with a linearly elastic solid.

This paper systematically compares the numerical implementation and computational cost between the Fourier spectral iterative perturbation method (FSIPM) and the finite element method (FEM) in solving partial differential equilibrium equations with inhomogeneous material coefficients and eigen-fields (e.g., stress-free strain and spontaneous electric polarization) involved in phase-field models. Four benchmark numerical examples, including inhomogeneous elastic, electrostatic, and steady-state heat conduction problems demonstrate that (1) the FSIPM rigorously requires uniform hexahedral (3D) and quadrilateral (2D) mesh and periodic boundary conditions for numerical implementation while the FEM permits arbitrary mesh and boundary conditions; (2) the FSIPM solutions are comparable to their FEM counterparts, and both of them agree with the analytic solutions, (3) the FSIPM is much faster in solving equilibrium equations than the FEM to achieve the accurate solutions, thus exhibiting a greater potential for large-scale 3D computations.

This paper introduces a unified concept and algorithm for the fractional-step (FS), artificial compressibility (AC) and pressure-projection (PP) methods for solving the incompressible Navier-Stokes equations. The proposed FSAC-PP approach falls into the group of pseudo-time splitting high-resolution methods incorporating the characteristics-based (CB) Godunov-type treatment of convective terms with PP methods. Due to the fact that the CB Godunov-type methods are applicable directly to the hyperbolic AC formulation and not to the elliptical FS-PP (split) methods, thus the straightforward coupling of CB Godunov-type schemes with PP methods is not possible. Therefore, the proposed FSAC-PP approach unifies the fully-explicit AC and semi-implicit FS-PP methods of Chorin including a PP step in the dual-time stepping procedure to a) overcome the numerical stiffness of the classical AC approach at (very) low and moderate Reynolds numbers, b) incorporate the accuracy and convergence properties of CB Godunov-type schemes with PP methods, and c) further improve the stability and efficiency of the AC method for steady and unsteady flow problems. The FSAC-PPmethod has also been coupled with a non-linear, full-multigrid and fullapproximation storage (FMG-FAS) technique to further increase the efficiency of the solution. For validating the proposed FSAC-PP method, computational examples are presented for benchmark problems. The overall results show that the unified FSAC-PP approach is an efficient algorithm for solving incompressible flow problems.

Recently, it was demonstrated that implicit solvent models were capable of generating stable B-form DNA structures. Specifically, generalized Born (GB) implicit solvent models have improved regarding the solvation of conformational sampling of DNA [1,2]. Here, we examine the performance of the GBSW and GBMV models in CHARMM for characterizing base flipping free energy profiles of undamaged and damaged DNA bases. Umbrella sampling of the base flipping process was performed for the bases cytosine, uracil and xanthine. The umbrella sampling simulations were carried-out with both explicit (TIP3P) and implicit (GB) solvent in order to establish the impact of the solvent model on base flipping. Overall, base flipping potential of mean force (PMF) profiles generated with GB solvent resulted in a greater free energy difference of flipping than profiles generated with TIP3P. One of the significant differences between implicit and explicit solvent models is the approximation of solute-solvent interactions in implicit solvent models. We calculated electrostatic interaction energies between explicit water molecules and the base targeted for flipping. These interaction energies were calculated over the base flipping reaction coordinate to illustrate the stabilizing effect of the explicit water molecules on the flipped-out state. It is known that nucleic base pair hydrogen bonds also influenced the free energy of flipping since these favorable interactions must be broken in order for a base to flip-out of the helix. The Watson-Crick base pair hydrogen bond fractions were calculated over the umbrella sampling simulation windows in order to determine the effect of base pair interactions on the base flipping free energy. It is shown that interaction energies between the flipping base and explicit water molecules are responsible for the lower base flipping free energy difference in the explicit solvent PMF profiles.

In this paper Lattice Boltzmann Method (LBM) has been used in order to perform Direct Numerical Simulation (DNS) for porous media analysis. Among the different configurations of porous media, open cell metallic foams are gaining a key role for a large number of applications, like heat exchangers for high performance cars or aeronautic components as well. Their structure allows improving heat transfer process with fruitful advantages for packaging issues and size reduction. In order to better understand metallic foam capabilities, a random sphere generation code has been implemented and fluid-dynamic simulations have been carried out by means of a kinetic approach. After having defined a computational domain the Reynolds number influence has been studied with the aim of characterizing both pressure drop and friction factor throughout a finite foam volume. In order to validate the proposed model, a comparison analysis with experimental data has been carried out too.

We investigate the ultra weak variational formulation (UWVF) of the 2-D Helmholtz equation using a new choice of basis functions. Traditionally the UWVF basis functions are chosen to be plane waves. Here, we instead use first kind Bessel functions. We compare the performance of the two bases. Moreover, we show that it is possible to use coupled plane wave and Bessel bases in the same mesh. As test cases we shall consider propagating plane and evanescent waves in a rectangular domain and a singular 2-D Helmholtz problem in an L-shaped domain.

This paper presents topology optimization of capillary, the typical two-phase flow with immiscible fluids, where the level set method and diffuse-interface model are combined to implement the proposed method. The two-phase flow is described by the diffuse-interface model with essential no slip condition imposed on the wall, where the singularity at the contact line is regularized by the molecular diffusion at the interface between two immiscible fluids. The level set method is utilized to express the fluid and solid phases in the flows and the wall energy at the implicit fluid-solid interface. Based on the variational procedure for the total free energy of two-phase flow, the Cahn-Hilliard equations for the diffuse-interface model are modified for the two-phase flow with implicit boundary expressed by the level set method. Then the topology optimization problem for the two-phase flow is constructed for the cost functional with general formulation. The sensitivity analysis is implemented by using the continuous adjoint method. The level set function is evolved by solving the Hamilton-Jacobian equation, and numerical test is carried out for capillary to demonstrate the robustness of the proposed topology optimization method. It is straightforward to extend this proposed method into the other two-phase flows with two immiscible fluids.

This is one of our series papers on multistep schemes for solving forward backward stochastic differential equations (FBSDEs) and related problems. Here we extend (with non-trivial updates) our multistep schemes in [W. Zhao, Y. Fu and T. Zhou, SIAM J. Sci. Comput., 36 (2014), pp. A1731-A1751] to solve the second-order FBSDEs (2FBSDEs). The key feature of the multistep schemes is that the Euler method is used to discretize the forward SDE, which dramatically reduces the entire computational complexity. Moreover, it is shown that the usual quantities of interest (e.g., the solution tuple (Yt,Zt,At,Γt) of the 2FBSDEs) are still of high order accuracy. Several numerical examples are given to show the effectiveness of the proposed numerical schemes. Applications of our numerical schemes to stochastic optimal control problems are also presented.

In this work, we present a model for an aerosol (air/particle mixture) in the respiratory system. It consists of the incompressible Navier-Stokes equations for the air and the Vlasov equation for the particles in a fixed or moving domain, coupled through a drag force. We propose a discretization of the model, investigate stability properties of the numerical code and sensitivity to parameter perturbation. We also focus on the influence of the aerosol on the airflow.

The swimming of a 3D fish-like body with finlets is numerically investigated at Re = 1000 (the Reynolds number is based on the uniform upstream flow and the length of the fish-like body). The finlets are simply modeled as thin rigid rectangular plates that undulate with the body. The wake structures and the flow around the caudal peduncle are studied. The finlets redirect the local flow across the caudal peduncle but the vortical structures in the wake are almost not affected by the finlets. Improvement of hydrodynamic performance has not been found in the simulation based on this simple model. The present numerical result is in agreement with that of the work of Nauen and Lauder [J. Exp. Biol., 204 (2001), pp. 2251-2263] and partially supports the hypothesis of Webb [Bull. Fish. Res. Bd. Can., 190 (1975), pp. 1-159].

High-order discretization techniques offer the potential to significantly reduce the computational costs necessary to obtain accurate predictions when compared to lower-order methods. However, efficient and universally-applicable high-order discretizations remain somewhat illusive, especially for more arbitrary unstructured meshes and for incompressible/low-speed flows. A novel, high-order, central essentially non-oscillatory (CENO), cell-centered, finite-volume scheme is proposed for the solution of the conservation equations of viscous, incompressible flows on three-dimensional unstructured meshes. Similar to finite element methods, coordinate transformations are used to maintain the scheme’s order of accuracy even when dealing with arbitrarily-shaped cells having non-planar faces. The proposed scheme is applied to the pseudo-compressibility formulation of the steady and unsteady Navier-Stokes equations and the resulting discretized equations are solved with a parallel implicit Newton-Krylov algorithm. For unsteady flows, a dual-time stepping approach is adopted and the resulting temporal derivatives are discretized using the family of high-order backward difference formulas (BDF). The proposed finite-volume scheme for fully unstructured mesh is demonstrated to provide both fast and accurate solutions for steady and unsteady viscous flows.

In this paper, a lattice Boltzmann BGK (LBGK) model is proposed for simulating incompressible axisymmetric flows. Unlike other existing axisymmetric lattice Boltzmann models, the present LBGK model can eliminate the compressible effects only with the small Mach number limit. Furthermore the source terms of the model are simple and contain no velocity gradients. Through the Chapman-Enskog expansion, the macroscopic equations for incompressible axisymmetric flows can be exactly recovered from the present LBGK model. Numerical simulations of the Hagen-Poiseuille flow, the pulsatile Womersley flow, the flow over a sphere, and the swirling flow in a closed cylindrical cavity are performed. The results agree well with the analytic solutions and the existing numerical or experimental data reported in some previous studies.