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.

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].

Despite its demonstrated importance in the deformation and dynamics of red blood cells, membrane viscosity has not received the same attention in computational models as elasticity and bending stiffness. Recent experiments on red blood cells indicated a power law response due to membrane viscosity. This is potentially much different from the solid viscoelastic models, such as Kelvin-Voigt and standard linear solid (SLS), currently used in computation to describe this aspect of the membrane. Within the context of a framework based on lattice Boltzmann and immersed boundary methods, we introduce SLS and power law models for membrane viscosity. We compare how the Kelvin-Voigt (as approximated by SLS) and power law models alter the deformation and dynamics of a spherical capsule in shear flows.

Moment equations provide a flexible framework for the approximation of the Boltzmann equation in kinetic gas theory. While moments up to second order are sufficient for the description of equilibrium processes, the inclusion of higher order moments, such as the heat flux vector, extends the validity of the Euler equations to non-equilibrium gas flows in a natural way.

Unfortunately, the classical closure theory proposed by Grad leads to moment equations, which suffer not only from a restricted hyperbolicity region but are also affected by non-physical sub-shocks in the continuous shock-structure problem if the shock velocity exceeds a critical value. Amore recently suggested closure theory based on the maximum entropy principle yields symmetric hyperbolic moment equations. However, if moments higher than second order are included, the computational demand of this closure can be overwhelming. Additionally, it was shown for the 5-moment system that the closing flux becomes singular on a subset of moments including the equilibrium state.

Motivated by recent promising results of closed-form, singular closures based on the maximum entropy approach, we study regularized singular closures that become singular on a subset of moments when the regularizing terms are removed. In order to study some implications of singular closures, we use a recently proposed explicit closure for the 5-moment equations. We show that this closure theory results in a hyperbolic system that can mitigate the problem of sub-shocks independent of the shock wave velocity and handle strongly non-equilibrium gas flows.

This work is a follow-up to our previous work. It extends and complements, both theoretically and experimentally, the results presented there. Under consideration is the homogenization of a model of a weakly random heterogeneous material. The material consists of a reference periodic material randomly perturbed by another periodic material, so that its homogenized behavior is close to that of the reference material. We consider laws for the random perturbations more general than in. We prove the validity of an asymptotic expansion in a certain class of settings. We also extend the formal approach introduced in. Our perturbative approach shares common features with a defect-type theory of solid state physics. The computational efficiency of the approach is demonstrated.

A new class of supersonic nonequilibrium flows is studied on the basis of solving the Boltzmann and model kinetic equations with the aim to consider new non-linear structures in open systems and to study anomalous transfer properties in relaxation zones. The Unified Flow Solver is applied for numerical simulations. Simple gases and gases with inner degrees of freedom are considered. The experimental data related to the influence of the so-called optical lattices on the supersonic molecular beams are considered and numerical analysis of the nonequilibrium states obtained on this basis is made. The nonuniform relaxation problem with these distributions is simulated numerically and anomalous transport is confirmed. The conditions for strong changes of the temperature in the anomalous transfer zones are discussed and are realized in computations.

We present a parallel Cartesian method to solve elliptic problems with complex immersed interfaces. This method is based on a finite-difference scheme and is second-order accurate in the whole domain. The originality of the method lies in the use of additional unknowns located on the interface, allowing to express straightforwardly the interface transmission conditions. We describe the method and the details of its parallelization performed with the PETSc library. Then we present numerical validations in two dimensions, assorted with comparisons to other related methods, and a numerical study of the parallelized method.

Stent placement is considered as a promising and minimally invasive technique to prevent rupture of aneurysm and favor coagulation mechanism inside the aneurysm. Many scholars study the effect of the stent on blood flow in cerebral aneurysm by numerical simulations, and usually regard blood as the Newtonian fluid, blood, however, is a kind of non-Newtonian fluid in practice. The main purpose of the present paper is to investigate the effect of non-Newtonian behavior on the hemodynamic characteristics of blood flow in stented cerebral aneurysm with lattice Boltzmann method. The Casson model is used to describe the blood non-Newtonian character, which is one of the most popular models in depicting blood fluid. In particular, hemodynamic characteristics derived with Newtonian and non-Newtonian models are studied, and compared in detail. The results show that the non-Newtonian effect gives a great influence on hemodynamic characteristics of blood flow in stented cerebral aneurysm, especially in small necked ones.

We study the construction of symplectic Runge-Kutta methods for stochastic Hamiltonian systems (SHS). Three types of systems, SHS with multiplicative noise, special separable Hamiltonians and multiple additive noise, respectively, are considered in this paper. Stochastic Runge-Kutta (SRK) methods for these systems are investigated, and the corresponding conditions for SRK methods to preserve the symplectic property are given. Based on the weak/strong order and symplectic conditions, some effective schemes are derived. In particular, using the algebraic computation, we obtained two classes of high weak order symplectic Runge-Kutta methods for SHS with a single multiplicative noise, and two classes of high strong order symplectic Runge-Kutta methods for SHS with multiple multiplicative and additive noise, respectively. The numerical case studies confirm that the symplectic methods are efficient computational tools for long-term simulations.

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.

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 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.

The Jiles-Atherton (J-A) model is a commonly used physics-based model in describing the hysteresis characteristics of ferromagnetic materials. However, citations and interpretation of this model in literature have been non-uniform. Solution methods for solving numerically this model has not been studied adequately. In this paper, through analyzing the mathematical properties of equations and the physical mechanism of energy conservation, we point out some unreasonable descriptions of this model and develop a relatively more accurate, modified J-A model together with its numerical solution method. Our method employs a fixed point method to compute anhysteretic magnetization. We obtain the susceptibility value of the anhysteretic magnetization analytically and apply the 4th order Runge-Kutta method to the solution of total magnetization. Computational errors are estimated and then precisions of the solving method in describing various materials are verified. At last, through analyzing the effects of the accelerating method, iterative error and step size on the computational errors, we optimize the numerical method to achieve the effects of high precision and short computing time. From analysis, we determine the range of best values of some key parameters for fast and accurate computation.

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.

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.

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.

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.

We analyze in this paper the pressure splitting scheme of a partitioned semi-implicit coupling algorithm for fluid-structure interaction (FSI) simulation. The semi-implicit coupling algorithm is developed on the ground of the artificial compressibility characteristic-based split (AC-CBS) scheme that serves not only for the fluid subsystem but also for the global FSI system. As the dual-time stepping procedure recommended for quasi-incompressible flows is incorporated into the implicit coupling stage, the fluctuating pressure may be unusually susceptible to the AC coefficient. Moreover, it is not trivial to devise an optimal AC formulation for pressure estimation. Instead, we consider a stabilized second-order pressure splitting scheme in the AC-CBS-based partitioned semi-implicit coupling algorithm. Computer simulation of a benchmark FSI experiment demonstrates that good agreement is exposed between the available and present data.