Our aim in this article is to improve the understanding of the colocated finite volume schemes for the incompressible Navier-Stokes equations. When all the variables are colocated, that means here when the velocities and the pressure are computed at the same place (at the centers of the control volumes), these unknowns must be properly coupled. Consequently, the choice of the time discretization and the method used to interpolate the fluxes at the edges of the control volumes are essentials. In the first and second parts of this article, two different time discretization schemes are considered with a colocated space discretization and we explain how the unknowns can be correctly coupled. Numerical simulations are presented in the last part of the article. This paper is not a comparison between staggered grid schemes and colocated schemes (for this, see, e.g., [15, 22]). We plan, in the future, to use a colocated space discretization and the multilevel method of [4] initially applied to the two dimensional Burgers problem, in order to solve the incompressible Navier-Stokes equations. One advantage of colocated schemes is that all variables share the same location, hence, the possibility to use hierarchical space discretizations more easily when multilevel methods are used. For this reason, we think that it is important to study this family of schemes.

A fourth-order finite difference method is proposed and studied for the primitive equations (PEs) of large-scale atmospheric and oceanic flow based on mean vorticity formulation. Since the vertical average of the horizontal velocity field is divergence-free, we can introduce mean vorticity and mean stream function which are connected by a 2-D Poisson equation. As a result, the PEs can be reformulated such that the prognostic equation for the horizontal velocity is replaced by evolutionary equations for the mean vorticity field and the vertical derivative of the horizontal velocity. The mean vorticity equation is approximated by a compact difference scheme due to the difficulty of the mean vorticity boundary condition, while fourth-order long-stencil approximations are utilized to deal with transport type equations for computational convenience. The numerical values for the total velocity field (both horizontal and vertical) are statically determined by a discrete realization of a differential equation at each fixed horizontal point. The method is highly efficient and is capable of producing highly resolved solutions at a reasonable computational cost. The full fourth-order accuracy is checked by an example of the reformulated PEs with force terms. Additionally, numerical results of a large-scale oceanic circulation are presented.

Weighted essentially non-oscillatory (WENO) methods have been developed to simultaneously provide robust shock-capturing in compressible fluid flow and avoid excessive damping of fine-scale flow features such as turbulence. Under certain conditions in compressible turbulence, however, numerical dissipation remains unacceptably high even after optimization of the linear component that dominates in smooth regions. Of the nonlinear error that remains, we demonstrate that a large fraction is generated by a "synchronization deficiency" that interferes with the expression of theoretically predicted numerical performance characteristics when the WENO adaptation mechanism is engaged. This deficiency is illustrated numerically in simulations of a linearly advected sinusoidal wave and the Shu-Osher problem [J. Comput. Phys., 83 (1989), pp. 32-78]. It is shown that attempting to correct this deficiency through forcible synchronization results in violation of conservation. We conclude that, for the given choice of candidate stencils, the synchronization deficiency cannot be adequately resolved under the current WENO smoothness measurement technique.

We study the biofilm-flow interaction resulting in biofilm growth, deformation and detachment phenomena in a cavity and shear flow using the phase field model developed recently [28]. The growth of the biofilm and the biofilm-flow interaction in various flow and geometries are simulated using an extended Newtonian constitutive model for the biofilm mixture in 2-D. The model predicts growth patterns consistent with experimental findings with randomly distributed initial biofilm colonies. Shear induced deformation, and detachment in biofilms is simulated in a shear cell. Rippling, streaming, and ultimate detachment phenomena in biofilms are demonstrated in the simulations, respectively, in a shear cell. Possible merging of detached biofilm blobs in oscillatory shear is observed in simulations as well. Detachment due to the density variation is also investigated shedding light on the possible bacteria induced detachment.

In this paper we develop a Stochastic Collocation Method (SCM) for flow in randomly heterogeneous porous media. At first, the Karhunen-Loève expansion is taken to decompose the log transformed hydraulic conductivity field, which leads to a stochastic PDE that only depends on a finite number of i.i.d. Gaussian random variables. Based on the eigenvalue decay property and a rough error estimate of Stroud cubature in SCM, we propose to subdivide the leading dimensions in the integration space for random variables to increase the accuracy. We refer to this approach as adaptive Stroud SCM. One- and two-dimensional steady-state single phase flow examples are simulated with the new method, and comparisons are made with other stochastic methods, namely, the Monte Carlo method, the tensor product SCM, and the quasi-Monte Carlo SCM. The results indicate that the adaptive Stroud SCM is more efficient and the statistical moments of the hydraulic head can be more accurately estimated.

Advanced Monte Carlo simulations of magnetisation and susceptibility in 3D XY model are performed at two different coupling constants β =0.55 and β =0.5, completing our previous simulation results with additional data points and extending the range of the external field to twice as small values as previously reported (h ≥ 0.00015625). The simulated maximal lattices sizes are also increased from L=384 to L=512. Our aim is an improved estimation of the exponent ρ, describing the Goldstone mode singularity M(h) = M(+0)+ch^ρ at h → 0, where M is the magnetisation. The data reveal some unexpected small oscillations. It makes the estimation by many-parameter fits of the magnetisation data unstable, and we are looking for an alternative method. Our best estimate ρ = 0.555(17) is extracted from the analysis of effective exponents determined from local fits of the susceptibility data. This method gives stable and consistent results for both values of β, taking into account the leading as well as the subleading correction to scaling. We report also the values of spontaneous magnetisation.

In this paper we propose a uniformly convergent numerical method for discretizing singularly perturbed nonlinear eigenvalue problems under constraints with applications in Bose-Einstein condensation and quantum chemistry. We begin with the time-independent Gross-Pitaevskii equation and show how to reformulate it into a singularly perturbed nonlinear eigenvalue problem under a constraint. Matched asymptotic approximations for the problem are presented to locate the positions and characterize the widths of boundary layers and/or interior layers in the solution. A uniformly convergent numerical method is proposed by using the normalized gradient flow and piecewise uniform mesh techniques based on the asymptotic approximations for the problem. Extensive numerical results are reported to demonstrate the effectiveness of our numerical method for the problems. Finally, the method is applied to compute ground and excited states of Bose-Einstein condensation in the semiclassical regime and some conclusive findings are reported. 

The structural, vibrational and electronic properties of warfarin sodium, warfarin and its metabolites have been investigated theoretically by performing the molecular mechanics (MM+ force field), the semi-empirical self-consistent-field molecular-orbital (AM1), and density functional theory calculations. The geometry of the molecules have been optimized, the vibrational dynamics and the electronic properties of the molecules have been calculated in their ground state in gas phase. 

For the backward diffusion equation, a stable discrete energy regularization algorithm is proposed. Existence and uniqueness of the numerical solution are given. Moreover, the error between the solution of the given backward diffusion equation and the numerical solution via the regularization method can be estimated. Some numerical experiments illustrate the efficiency of the method, and its application in image deblurring.

In [3], Chan and Wong proposed to use total variational regularization for both images and point spread functions in blind deconvolution. Their experimental results show that the detail of the restored images cannot be recovered. In this paper, we consider images in Lipschitz spaces, and propose to use Lipschitz regularization for images and total variational regularization for point spread functions in blind deconvolution. Our experimental results show that such combination of Lipschitz and total variational regularization methods can recover both images and point spread functions quite well.