The commonly used incompressible phase field models for non-reactive, binary fluids, in which the Cahn-Hilliard equation is used for the transport of phase variables (volume fractions), conserve the total volume of each phase as well as the material volume, but do not conserve the mass of the fluid mixture when densities of two components are different. In this paper, we formulate the phase field theory for mixtures of two incompressible fluids, consistent with the quasi-compressible theory [28], to ensure conservation of mass and momentum for the fluid mixture in addition to conservation of volume for each fluid phase. In this formulation, the mass-average velocity is no longer divergence-free (solenoidal) when densities of two components in the mixture are not equal, making it a compressible model subject to an internal con-straint. In one formulation of the compressible models with internal constraints (model 2), energy dissipation can be clearly established. An efficient numerical method is then devised to enforce this compressible internal constraint. Numerical simulations in confined geometries for both compressible and the incompressible models are carried out using spatially high order spectral methods to contrast the model predictions. Numerical comparisons show that (a) predictions by the two models agree qualitatively in the situation where the interfacial mixing layer is thin; and (b) predictions differ significantly in binary fluid mixtures undergoing mixing with a large mixing zone. The numerical study delineates the limitation of the commonly used incompressible phase field model using volume fractions and thereby cautions its predictive value in simulating well-mixed binary fluids.

An alternate BGK type formulation of the Enskog equation has been recently proposed. It was shown that the new model has a valid H-theorem and correct thermal conductivity. We propose Lattice Boltzmann (LB) formulation of this new Enskog-BGK model. The molecular nature of the model is verified in case of shear flow by comparing the predicted normal stress behavior by the current model with the prediction of molecular dynamics simulations. We extend the model for multiphase flow by incorporating attractive part as Vlasov type force. To validate multiphase formulation, the results of 3D simulations of a condensing bubble in a periodic box are presented.

Recently, a new differential discontinuous formulation for conservation laws named the Correction Procedure via Reconstruction (CPR) is developed, which is in-spired by several other discontinuous methods such as the discontinuous Galerkin (DG), the spectral volume (SV)/spectral difference (SD) methods. All of them can be unified under the CPR formulation, which is relatively simple to implement due to its finite-difference-like framework. In this paper, a different discontinuous solution space including both polynomial and Fourier basis functions on each element is employed to compute broad-band waves. Free-parameters introduced in the Fourier bases are optimized to minimize both dispersion and dissipation errors through a wave propagation analysis. The optimization procedure is verified with a mesh resolution analysis. Numerical results are presented to demonstrate the performance of the optimized CPR formulation.

In this article the instabilities appearing in a liquid layer are studied numerically by means of the linear stability method. The fluid is confined in an annular pool and is heated from below with a linear decreasing temperature profile from the inner to the outer wall. The top surface is open to the atmosphere and both lateral walls are adiabatic. Using the Rayleigh number as the only control parameter, many kind of bifurcations appear at moderately low Prandtl numbers and depending on the Biot number. Several regions on the Prandtl-Biot plane are identified, their boundaries being formed from competing solutions at codimension-two bifurcation points.

The definition of a molecular surface which is physically sound and computationally efficient is a very interesting and long standing problem in the implicit solvent continuum modeling of biomolecular systems as well as in the molecular graphics field. In this work, two molecular surfaces are evaluated with respect to their suitability for electrostatic computation as alternatives to the widely used Connolly-Richards surface: the blobby surface, an implicit Gaussian atom centered surface, and the skin surface. As figures of merit, we considered surface differentiability and surface area continuity with respect to atom positions, and the agreement with explicit solvent simulations. Geometric analysis seems to privilege the skin to the blobby surface, and points to an unexpected relationship between the non connectedness of the surface, caused by interstices in the solute volume, and the surface area dependence on atomic centers. In order to assess the ability to reproduce explicit solvent results, specific software tools have been developed to enable the use of the skin surface in Poisson-Boltzmann calculations with the DelPhi solver. The results indicate that the skin and Connolly surfaces have a comparable performance from this last point of view.

We propose to extend the d’Humieres version of the lattice Boltzmann scheme to triangular meshes. We use Bravais lattices or more general lattices with the property that the degree of each internal vertex is supposed to be constant. On such meshes, it is possible to define the lattice Boltzmann scheme as a discrete particle method, without need of finite volume formulation or Delaunay-Voronoi hypothesis for the lattice. We test this idea for the heat equation and perform an asymptotic analysis with the Taylor expansion method for two schemes named D2T4 and D2T7. The results show a convergence up to second order accuracy and set new questions concerning a possible super-convergence.

This paper proposes a variational binary level set method for shape and topology optimization of structural. First, a topology optimization problem is pre-sented based on the level set method and an algorithm based on binary level set method is proposed to solve such problem. Considering the difficulties of coordination between the various parameters and efficient implementation of the proposed method, we present a fast algorithm by reducing several parameters to only one parameter, which would substantially reduce the complexity of computation and make it easily and quickly to get the optimal solution. The algorithm we constructed does not need to re-initialize and can produce many new holes automatically. Furthermore, the fast algorithm allows us to avoid the update of Lagrange multiplier and easily deal with constraints, such as piecewise constant, volume and length of the interfaces. Finally, we show several optimum design examples to confirm the validity and efficiency of our method.

Salt influences protein stability through electrostatic mechanisms as well as through nonpolar Hofmeister effects. In the present work, a continuum solvation based model is developed to explore the impact of salt on protein stability. This model relies on a traditional Poisson-Boltzmann (PB) term to describe the polar or electrostatic effects of salt, and a surface area dependent term containing a salt concentration dependent microscopic surface tension function to capture the non-polar Hofmeister effects. The model is first validated against a series of cold-shock protein variants whose salt-dependent protein fold stability profiles have been previously determined experimentally. The approach is then applied to HIV-1 protease in order to explain an experimentally observed enhancement in stability and activity at high (1M) NaCl concentration. The inclusion of the salt-dependent non-polar term brings the model into quantitative agreement with experiment, and provides the basis for further studies into the impact of ionic strength on protein structure, function, and evolution.

In this paper, we consider variational approaches to handle the multiplicative noise removal and deblurring problem. Based on rather reasonable physical blurring-noisy assumptions, we derive a new variational model for this issue. After the study of the basic properties, we propose to approximate it by a convex relaxation model which is a balance between the previous non-convex model and a convex model. The relaxed model is solved by an alternating minimization approach. Numerical examples are presented to illustrate the effectiveness and efficiency of the proposed method.

We study efficient spectral-collocation and continuation methods (SCCM) for rotating two-component Bose-Einstein condensates (BECs) and rotating two-component BECs in optical lattices, where the second kind Chebyshev polynomials are used as the basis functions for the trial function space. A novel two-parameter continuation algorithm is proposed for computing the ground state and first excited state solutions of the governing Gross-Pitaevskii equations (GPEs), where the classical tangent vector is split into two constraint conditions for the bordered linear systems. Numerical results on rotating two-component BECs and rotating two-component BECs in optical lattices are reported. The results on the former are consistent with the published numerical results.

This paper summarizes the mathematical and numerical theories and computational elements of the adaptive fast multipole Poisson-Boltzmann (AFMPB) solver. We introduce and discuss the following components in order: the Poisson-Boltzmann model, boundary integral equation reformulation, surface mesh generation, the nodepatch discretization approach, Krylov iterative methods, the new version of fast multipole methods (FMMs), and a dynamic prioritization technique for scheduling parallel operations. For each component, we also remark on feasible approaches for further improvements in efficiency, accuracy and applicability of the AFMPB solver to large-scale long-time molecular dynamics simulations. The potential of the solver is demonstrated with preliminary numerical results.

Spectral element methods on simplicial meshes, say TSEM, show both the advantages of spectral and finite element methods, i.e., spectral accuracy and geometrical flexibility. We present aTSEM solver of the two-dimensional (2D) incompressible Navier-Stokes equations, with possible extension to the 3D case. It uses a projection method in time and piecewise polynomial basis functions of arbitrary degree in space. The so-called Fekete-Gauss TSEM is employed,i.e., Fekete (resp. Gauss) points of the triangle are used as interpolation (resp. quadrature) points. For the sake of consistency, isoparametric elements are used to approximate curved geometries. The resolution algorithm is based on an efficient Schur complement method, so that one only solves for the element boundary nodes. Moreover, the algebraic system is never assembled, therefore the number of degrees of freedom is not limiting. An accuracy study is carried out and results are provided for classical benchmarks: the driven cavity flow, the flow between eccentric cylinders and the flow past a cylinder.

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.

We propose a mathematically rigorous method to measure the spontaneous curvature of a bilayer membrane by molecular dynamics (MD) simulation, which provides description of the molecular mechanisms that cause the spontaneous curvature. As a main result, for the membrane setup investigated, the spontaneous curvature is proved to be a constant plus twice the mean curvature of the membrane in its tensionless ground state. The spontaneous curvature due to the built-in transbilayer asymmetry of the membrane in terms of lipid shape is studied by the proposed method. A linear dependence of the spontaneous curvature with respect to the head-bead diameter difference and the lipid mixing ratio is discovered. The consistency with the theoretical results provides evidence supporting the validity of our method.

Algorithms for adaptive mesh refinement using a residual error estimator are proposed for fluid flow problems in a finite volume framework. The residual error estimator, referred to as the ℜ-parameter is used to derive refinement and coarsening criteria for the adaptive algorithms. An adaptive strategy based on the ℜ-parameter is proposed for continuous flows, while a hybrid adaptive algorithm employing a combination of error indicators and the ℜ-parameter is developed for discontinuous flows. Numerical experiments for inviscid and viscous flows on different grid topologies demonstrate the effectiveness of the proposed algorithms on arbitrary polygonal grids.

Gases in microfluidic structures or devices are often in a non-equilibrium state. The conventional thermodynamic models for fluids and heat transfer break down and the Navier-Stokes-Fourier equations are no longer accurate or valid. In this paper, the extended thermodynamic approach is employed to study the rarefied gas flow in microstructures, including the heat transfer between a parallel channel andpressure-driven Poiseuille flows through a parallel microchannel andcircular microtube. The gas flow characteristics are studied and it is shown that the heat transfer in the non-equilibrium state no longer obeys the Fourier gradient transport law. In addition, the bimodal distribution of streamwise and spanwise velocity and temperature through a long circular microtube is captured for the first time.

We recently developed the Image-Charge Solvation Model (ICSM), which is an explicit/implicit hybrid model to accurately account for long-range electrostatic forces in molecular dynamics simulations [Lin et al., J. Chem. Phys., 131,154103,2009]. The ICSM has a productive spherical volume within the simulation cell for which key physical properties of bulk water are reproduced, such as density, radial distribution function, diffusion constants and dielectric properties. Although the reaction field (RF) is essential, it typically accounts for less than 2% of the total electrostatic force on a water molecule. This observation motivates investigating further the role of the RF within the ICSM. In this report we focus on distributions of forces and torques on water molecules as a function of distance from the origin and make extensive tests over a range of model parameters where Coulomb forces are decomposed into direct interactions from waters modeled explicitly and the RF. Molecular torques due to the RF typically account for 20% of the total torque, revealing why the RF plays an important role in the dielectric properties of simulated water. Moreover, it becomes clear that the buffer layer in the ICSM is essential to mitigate artifacts caused by the discontinuous change in dielectric constants at the explicit/implicit interface.

In this paper an explicit finite-difference time-domain scheme for solving the Maxwell’s equations in non-staggered grids is presented. The proposed scheme for solving the Faraday’s and Ampere’s equations in a theoretical manner is aimed to preserve discrete zero-divergence for the electric and magnetic fields. The inherent local conservation laws in Maxwell’s equations are also preserved discretely all the time using the explicit second-order accurate symplectic partitioned Runge-Kutta scheme. The remaining spatial derivative terms in the semi-discretized Faraday’s and Ampere’s equations are then discretized to provide an accurate mathematical dispersion relation equation that governs the numerical angular frequency and the wavenumbers in two space dimensions. To achieve the goal of getting the best dispersive characteristics, we propose a fourth-order accurate space centered scheme which minimizes the difference between the exact and numerical dispersion relation equations. Through the computational exercises, the proposed dual-preserving solver is computationally demonstrated to be efficient for use to predict the long-term accurate Maxwell’s solutions.

A multi-dimensionally upwind conservative Residual Distribution algorithm for simulating viscous axisymmetric hypersonic flows in thermo-chemical nonequilibrium on unstructured grids is presented and validated in the case of the complex flow-field over a double cone configuration. The resulting numerical discretization combines a state-of-the-art nonlinear quasi-monotone second order blended scheme for distributing the convective residual and a standard Galerkin formulation for the diffusive residual. The physical source terms are upwinded together with the convective fluxes. Numerical results show an excellent agreement with experimental measurements and available literature.

The onset of cavitating conditions inside the nozzle of liquid injectors is known to play a major role on spray characteristics, especially on jet penetration and break-up. In this work, we present a Direct Numerical Simulation (DNS) based on the Lattice Boltzmann Method (LBM) to study the fluid dynamic field inside the nozzle of a cavitating injector. The formation of the cavitating region is determined via a multi-phase approach based on the Shan-Chen equation of state. The results obtained by the LBM simulation show satisfactory agreement with both numerical and experimental data. In addition, numerical evidence of bubble break-up, following upon flow-induced cavitation, is also reported.