
Citation: Bhushan Sopori, Srinivas Devayajanam, Prakash Basnyat. Surface characteristics and damage distributions of diamond wire sawn wafers for silicon solar cells[J]. AIMS Materials Science, 2016, 3(2): 669-685. doi: 10.3934/matersci.2016.2.669
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The chemotaxis refers to the collective motion of bacteria, cells or an organisms in response to an attractant gradient. There are numerous examples of chemotaxis in animal and insect ecology, biological and biomedical sciences [9]. Deep understanding of the behavior of chemotaxis phenomenon is of great significance to the biological and medical applications.
Various kinds of mathematical models have been developed by both experimentalists and theoreticians to describe the chemotactic phenomenon. In addition, to further describe and interpret the bioconvection phenomenon [14], a variety of coupled chemotaxis-fluid models have been proposed and studied in [5,8,24]. The coupled model is expressed as follows:
$ ∂n∂t+∇⋅(un)=Dn∇2n−χ∇⋅[r(c)n∇c], $
|
(1) |
$ ∂c∂t+∇⋅(uc)=Dc∇2c−nκr(c), $
|
(2) |
$ ρ(∂u∂t+u⋅∇u)=−∇p+η∇2u+nVb(ρb−ρ)g, $
|
(3) |
$ ∇⋅u=0. $
|
(4) |
Here,
It can be seen from the above system that the chemotaxis-fluid model involves highly nonlinearity coupled with chemotaxis, diffusion and convection, which brings great difficulties to get the analytical solution. Recently, several numerical methods have been developed to study the chemotaxis phenomenon, such as finite element, finite volume schemes [13,21], upwind-difference potentials method [10], fractional step algorithms [20,25], interior penalty/discontinuous Galerkin methods [11,12], and cell-overcrowding prevention models [1,7], etc. In the work by Chertock et al. [5], a coupled chemotaxis-fluid system has been numerically studied by a high-resolution vorticity-based hybrid finite-volume finite-difference scheme. In [22], the chemotaxis phenomenon in incompressible viscous fluid has been numerically studied by a compact finite difference scheme. The plume patterns were studied by solving a chemotaxis-diffusion-convection coupling system in [6], where the comparison of different systems of chemotaxis-diffusion-convection, Rayleigh-B
In this work, we will develop an efficient LBM to solve the coupled chemotaxis-fluid model. LBM originates from kinetic Boltzmann equation, which has been successfully applied in modeling complex fluid flows [18,4,2]. In addition, LBM also shows its excellent capability in solving the nonlinear systems [23,3,28,26]. For the chemotaxis problem, a simplified LBM was developed for a bacterial chemotaxis model by Hilpert [16]. While, Yan et al. [27] developed a MRT-LBM to investigate the traveling bacterial bands of chemotactic bacteria. However, due to the highly nonlinearity of the coupled chemotaxis-fluid model, we need to develop more accurate and stable LBM to solve this complex problem. In [19], a novel MRT-LBM was proposed to simulate multi-phase fluids with Peng-Robinson (P-R) equation of state. To enhance the stability of the MRT-LBM, B-W scheme is introduced in the discretization of the evolution equation. Numerical results showed that the P-R free energy model was solved precisely and spurious currents were eliminated effectively. Inspired by this, we will apply the MRT-LBM with B-W scheme to solve the coupled chemotaxis-fluid model.
The rest of this article is organized as follows. In Section Ⅱ, the MRT-LBM with B-W scheme for the chemotaxis-fluid model is proposed. In Section Ⅲ, several numerical experiments are carried out on different chemotaxis problems, including the classical K-S model, the coupled Navier-Stokes-Keller-Segel (NS-KS) model, and the bacterial biocovection problem. The paper ends with some conclusions in Section Ⅳ.
In this section, we will introduce the MRT-LBM with B-W scheme for the coupled chemotaxis-fluid model (1)-(4). To better investigate the coupled chemotaxis-fluid model, the following dimensionless form is taken:
$ x′=xL,t′=DnL2t,c′=ccair,n′=nnr,u′=LDnu,p′=L2ηDnp,g′=gg, $
|
where
$ ∂n∂t+∇⋅(un)=∇2n−α∇⋅[r(c)n∇c], $
|
(5) |
$ ∂c∂t+∇⋅(uc)=δ∇2c−βr(c)n, $
|
(6) |
$ ∂u∂t+u⋅∇u=−∇p+Sc∇2u+γScnz. $
|
(7) |
$ ∇⋅u=0, $
|
(8) |
where
$ r(c) = \frac{1}{2}(1+ \frac{c-c^*}{\sqrt{(c-c*)^2}+\epsilon^2}), $ |
where
The dimensionless parameters
$ α=χcairDn,β=κnrL2cairDn,γ=Vbnrg(ρb−ρ)L3ηDn,δ=DcDn,Sc=ηDnρ. $
|
In this section, LBM with MRT collision operator is applied to solve the incompressible N-S equations (7)-(8). To capture the chemotaxis phenomenon more accurately, B-W scheme is introduced in the discretization of the evolution equation of MRT-LBM.
The discrete velocity Boltzmann equation with MRT collision operator is expressed as
$ ∂hi∂t+ˆcei⋅∇hi=−Λij[hj−heqj]+Hi, $
|
(9) |
where,
The discrete velocity Boltzmann equation (9) is solved by a time-splitting scheme, which is decomposed into two sub-processes, i.e., the collision process,
$ ∂hi∂t=−Λij[hj−heqj]+Hi, $
|
(10) |
and the streaming process,
$ ∂hi∂t+ˆcei⋅∇hi=0. $
|
(11) |
In the MRT model, the collision subprocess is carried out in the moment space. We take the generally used D2Q9 (two-dimensional space with nine discrete velocities) model as an example. The distribution functions
$ \mathbf{m} = \mathbf{M} \cdot \mathbf{h} = (\rho, e, \varepsilon, j_x, q_x, j_y, q_y, p_{xx}, p_{xy})^T, $ |
where
$ \mathbf{M} = \left( {111111111−4−1−1−1−122224−2−2−2−21111010−101−1−110−20201−1−110010−111−1−100−20211−1−101−11−10000000001−11−1 } \right). $
|
Through multiplying the transformation matrix
$ ∂m∂t=−˜S(m−meq)+ˆH, $
|
(12) |
where
$ \mathbf{\widetilde{S}} = \mathrm{diag}\{\widetilde{s}_0, \widetilde{s}_1, \widetilde{s}_2, \widetilde{s}_3, \widetilde{s}_4, \widetilde{s}_5, \widetilde{s}_6, \widetilde{s}_7, \widetilde{s}_8\}. $ |
The equilibrium moment
$ meq=M⋅heq=ρ[1−2+3u21−3u2u−uv−vu2−v2uv]. $
|
(13) |
$ ˆH0=0,ˆH1=6(1−s12)u⋅Ft,ˆH2=−6(1−s22)u⋅Ft,ˆH3=Ftx,ˆH4=−(1−s42)Ftx,ˆH5=Fty,ˆH6=−(1−s62)Fty,ˆH7=2(1−s72)(uFtx−vFty),ˆH8=(1−s82)(uFty+vFtx), $
|
(14) |
where
$ \mathbf{F}_t = (F_{tx}, F_{ty}). $ |
In this simulation,
$ Ft=γScnz. $
|
(15) |
The first order explicit Euler scheme is used to discrete (12) as
$ m+=m−S(m−meq)+δtˆH, $
|
(16) |
where
$ \mathbf{S} = \mathrm{diag}\{s_0, s_1, s_2, s_3, s_4, s_5, s_6, s_7, s_8\}. $ |
In simulations,
Next, through using the second-order B-W scheme, Eq. (11) can be solved on a regular lattice with spacing
$ hi(x,t+δt)=h+i(x,t)−A2(3h+i(x,t)−4h+i(x−eiδx,t)+h+i(x−2eiδx,t))+A22(h+i(x,t)−2h+i(x−eiδx,t)+h+i(x−2eiδx,t)), $
|
(17) |
where the time step
The macroscopic quantities,
$ ρ=∑ihi,ρu=∑icihi+δt2Ft. $
|
(18) |
The evolution equations of the LBM for (5) and (6) are given by
$ ∂fi∂t+ˆci⋅∇fi=−1τn(fi−feqi)+Si, $
|
(19) |
$ ∂gi∂t+ˆci⋅∇gi=−1τc(gi−geqi)+ˆSi+δt2∂tˆSi, $
|
(20) |
where
$ Si=ωiˆci⋅Br(c)n∇c,ˆSi=ωi(−βr(c)n). $
|
Here,
$ feqi(x,t)=ωin(1+ˆci⋅uc2s),geqi(x,t)=ωic(1+ˆci⋅uc2s). $
|
(19) and (20) are decomposed into two sub-processes: the collision process
$ ∂fi∂t=−1τn(fi−feqi)+Si, $
|
(21) |
$ ∂gi∂t=−1τc(gi−geqi)+ˆSi+δt2∂tˆSi, $
|
(22) |
and the streaming process,
$ ∂fi∂t+ˆci⋅∇fi=0, $
|
(23) |
$ ∂gi∂t+ˆci⋅∇gi=0. $
|
(24) |
The first order explicit Euler scheme is used to solve the collision process (21)-(22), which leads to
$ f+i=fi−δtτn(fi−feqi)+δtSi,g+i=gi−δtτc(gi−geqi)+δtˆSi+δt22∂tˆSi. $
|
B-W scheme is used to solve (23) and (24),
$ fi(x,t+δt)=f+i(x,t)−A2(3f+i(x,t)−4f+i(x−eiδx,t)+f+i(x−2eiδx,t))+A22(f+i(x,t)−2f+i(x−eiδx,t)+f+i(x−2eiδx,t)), $
|
(25) |
$ gi(x,t+δt)=g+i(x,t)−A2(3g+i(x,t)−4g+i(x−eiδx,t)+g+i(x−2eiδx,t))+A22(g+i(x,t)−2g+i(x−eiδx,t)+g+i(x−2eiδx,t)). $
|
(26) |
The concentrations of the bacteria
$ n(x,t)=∑ifi(x,t),c(x,t)=∑igi(x,t). $
|
To validate that the stability is improved by the present LBM with B-W scheme, and also to verify the capability of the proposed method, a series of chemotaxis problems are numerically investigated. In the following numerical experiments, the general bounce-back scheme in reference [29] is used to treat the macroscopic boundary conditions in the LBM with B-W scheme.
In this section, the following classical K-S chemotaxis problem is considered.
$ ∂n∂t=μ∇⋅n−χ∇⋅(n∇c), $
|
(27) |
$ ∂c∂t=∇2c+n−c. $
|
(28) |
(27)-(28) can be regarded as a special case of the generalized K-S model.
$ n(x, y, 0) = 1000e^{ - 100(x^2 + y^2 )}, \quad c(x, y, 0) = 500e^{ - 50(x^2 +y^2 )}. $ |
The boundary conditions are
$ {{\partial n} \over {\partial \mathbf{v}}} = {{\partial c} \over {\partial \mathbf{v}}} = 0, (x, y) \in \partial \Omega, $ |
where
Under above initial and boundary conditions, the solution of (27)-(28) will blow up at the origin in finite time, which brings a great challenge in the numerical simulation. To illustrate that the stability is improved by B-W scheme, the comparison between standard LBM and the present LBM with B-W scheme is carried out. In the numerical experiment, the D2Q9 lattice model is used with a
In this section, the incompressible N-S equations coupled with K-S equation is solved for the convergence test of the proposed LBM with B-W scheme. The mathematical model has the following form,
$ ∂n∂t+∇⋅(un)=∇2n−∇⋅[χn∇c],∂c∂t+∇⋅(uc)=∇2c+nf(c)−cκ, $
|
$ ∂u∂t+u⋅∇u=−∇p+μ∇2u, $
|
(29) |
$ ∇⋅u=0. $
|
(30) |
In the numerical simulation,
$ ∂n∂v=∂c∂v=∂p∂v=0,u=uexact,(x,y)∈∂Ω. $
|
The computational domain is
$ uexact=−cos(πx)sin(πy)e−2π2t,vexact=−sin(πx)cos(πy)e−2π2t,p=c1−0.25(cos(2πx)+cos(2πy))e−4π2t,nexact=cos(πx)cos(πy)e−π2t,cexact=cos(πx)cos(πy)e−2π2t. $
|
To measure the accuracy, the following relative error is applied:
$ E=Σ|ϕ(x,t)−ϕ∗(x,t)|Σ|ϕ∗(x,t)|, $
|
where
It can be seen from Table 1 that numerical solutions of
order | order | order | ||||
– | – | – | ||||
1.9172 | 1.9130 | 1.9139 | ||||
1.9580 | 1.9560 | 1.9560 | ||||
1.9788 | 1.9772 | 1.9779 |
The chemotaxis response of bacterial suspensions can be described by the chemotaxis-fluid model (5)-(8). The balance between chemotaxis, diffusion, and convection of bacteria leads to the formation and stability of plumes. There still needs to a deep understanding of the particular impact of each mechanism.
In the simulations, the parameters of (5)-(8) are set as
$ n0(x,y)={1,ify>0.501−0.01(sin(x−0.5)π)),0.5,otherwise,c0(x,y)=1,u0(x,y)=0, $
|
At the top boundary
$ χnr(c)cy−Dnny=0,c=1.0,v=0,uy=0,∀(x,y)∈∂Ωtop, $
|
(31) |
where
$ ny=cy=0,u=v=0,∀(x,y)∈∂Ωbot. $
|
(32) |
The mixed boundary condition in Eq. (31) can be regrouped as
First of all, as the numerical experiments in [17], the case of
In this subsection, the system (5)-(8) on the rectangular domain is numerically studied. In the following numerical simulations, the coefficients are set as
As in [17], the following initial data is considered:
$ n0(x,y)=0.8+0.2rand(),c0(x,y)=1,u0(x,y)=0, $
|
where rand() is a random number uniformly distributed in the interval [0, 1].
The evolution of the cell density
In this subsection, the effect of the parameter
$ n0(x,y)={1,ify>0.499−0.05(sin(x−0.5)π))0.5,otherwise,c0(x,y)=1,u0(x,y)=0. $
|
The computational domain is
Numerical results of
An accurate and stable MRT-LBM with B-W scheme for a chemotaxis-fluid model is developed. Through introducing B-W scheme in the evolution process of the LBM, the numerical stability is improved. The numerical study of the classical K-S model shows that the proposed LBM with B-W scheme could preserve the positivity of bacteria concentrations. Then, the second order accuracy is tested by simulating the coupled NS-KS model. The nonlinear dynamics of the chemotaxis-fluid model was investigated numerically by the proposed MRT-LBM with B-W scheme. Our numerical results agree well with those in the literature under different settings. In the numerical simulation of bioconvection phenomenon, the evolution of the instability of falling plumes and the convergence towards numerically stable stationary plumes are observed.
Rewritten the evolution equation (17) up to
$ hi(x,t+δt)=h+i(x,t)−δtcei⋅∇h+i(x,t)+12δt2(cei⋅∇)2h+i(x,t)+O(δx3). $
|
(33) |
Multiplying Eq. (16) by inverse of the transformation matrix
$ ∂thi+cei⋅∇hi=Ωi−δt2[∂2thi−(cei⋅∇)2hi+2cei⋅∇Ωi]+O(δx2+δt2), $
|
(34) |
where
$ ∂2thi=(cei⋅∇)2hi+∂tΩi−cei⋅∇Ωi+O(δt). $
|
(35) |
Thus, Eq. (34) can be rewritten as
$ Dihi=(1−δt2Di)Ωi+O(δx2+δt2), $
|
(36) |
where
In addition, from Eq. (34), we can see that
$ Dihi+δt2D2ihi=−Λij[hj−heqj]+Hi+O(δx2+δt2). $
|
(37) |
Then we introduce the following expansions:
$ hi=h(0)i+εh(1)i+ε2h(2)i+⋯,∂∂t=ε∂∂t1+ε2∂∂t2,∇=ε∇1,Hi=εH(1)i, $
|
(38) |
where
$ O(ε0):h(0)i=h(eq)i, $
|
(39a) |
$ O(ε1):D1ih(eq)i=−Λijh(1)j+H(1)i, $
|
(39b) |
$ O(ε1):∂t2h(0)i+D1i[(Iij−Λij2)h(1)j]=−Λijh(2)j−δt2D1iH(1)i, $
|
(39c) |
where
Multiplying the transformation Matrix
$ O(ε0):m(0)=m(eq), $
|
(40a) |
$ O(ε1):D1m(0)=−˜Sm(1)+ˆH(1), $
|
(40b) |
$ O(ε2):∂t2m(0)+D1(I−S2)m(1)+δt2D1ˆH(1)=−˜Sm(2), $
|
(40c) |
where
In addition, from Eqs. (18) and (40a), we derive
$ ρ(1)=0,j(1)x=−δt2F(1)tx,j(1)y=−δt2F(1)ty,ρ(k)=j(k)x=j(k)y=0,k>1. $
|
(41) |
On the
$ ∂t1[ρρ(−2+3u2)ρ(1−3u2)ρu−ρuρv−ρvρ(u2−v2)ρuv]+∂1x[ρu0−ρuc2sρ+ρu2ρBx/3ρuvρuv2ρu/3ρv/3]+∂1y[ρv0−ρvρuvρuvc2sρ+ρv2ρBy/3−2ρv/3ρu/3]=[0−˜s1e(1)−˜s2ε(1)0−˜s4q(1)x0−˜s6q(1)y−˜s7p(1)xx−˜s8p(1)xy]+[06(1−s1/2)u⋅F(1)t−6(1−s2/2)u⋅F(1)tF(1)tx−(1−s4/2)F(1)txF(1)ty−(1−s6/2)F(1)ty2(1−s7/2)(uF(1)tx−vF(1)ty)(1−s8/2)(uF(1)ty+vF(1)tx)] $
|
(42) |
where
Similarly, From Eq. (40b), the scale equations of conserved quantities
$ ∂t2ρ=0. $
|
(43) |
$ ∂t2(ρu)+16(1−s12)∂1xe(1)+(1−s72)(12∂1xp(1)xx+∂1yp(1)xy)+δt2(1−s12)∂1x(u⋅F(1)t)+δt2(1−s72)∂1x(uF(1)tx−vF(1)ty)+δt2(1−s82)∂1y(uF(1)ty+vF(1)tx)=0, $
|
(44) |
$ ∂t2(ρv)+16(1−s12)∂1ye(1)+(1−s72)(∂1xp(1)xy−12∂1yp(1)xx)+δt2(1−s72)∂1x(uF(1)ty+vF(1)tx)+δt2(1−s12)∂1y(u⋅F(1)t)−δt2(1−s72)∂1y(uF(1)tx−vF(1)ty)=0. $
|
(45) |
To close the hydrodynamic equations at the second order of
$ e(1)=−1˜s1[2ρ(∂1xu+∂1yv)+3s1u⋅F(1)t]+O(Ma3), $
|
(46) |
$ p(1)xx=−1˜s7[23ρ(∂1xu−∂1yv)+s7(uF(1)tx−vF(1)ty)]+O(Ma3), $
|
(47) |
$ p(1)xy=−1˜s8[13ρ(∂1xv+∂1yu)+s82(uF(1)ty+vF(1)tx)]+O(Ma3). $
|
(48) |
With Eqs. (46), (47) and (48), we can obtain the hydrodynamic equations at
Continuity equations
$ ∂t1ρ+∂1x(ρu)+∂1y(ρv)=0, $
|
(49) |
$ ∂t2ρ=0. $
|
(50) |
Momentum equations
$ ∂t1ρu+∂1x(c2sρ+ρu2)+∂1y(ρuv)=F(1)tx, $
|
(51) |
$ ∂t1ρv+∂1x(ρuv)+∂1y(c2sρ+ρv2)=F(1)ty, $
|
(52) |
$ ∂t2(ρu)=∂1x(ρν(∂1xu−∂1yv)+ρζ(∂1xu+∂1yv))+∂1y(ρν(∂1xv+∂1yu)), $
|
(53) |
$ ∂t2(ρv)=∂1x(ρν(∂1xv+∂1yu))+∂1y(ρν(∂1yv−∂1xu)+ρζ(∂1xu+∂1yv)), $
|
(54) |
where
Combining the above equations on
$ ∂tρ+∇⋅(ρu)=0, $
|
(55) |
$ ∂ρu∂t+∇⋅(ρu⊗u)=−∇c2sρ+∇⋅[ρν(∇u+∇uT)+ρ(ζ−ν)(∇⋅u)I]+Ft. $
|
(56) |
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order | order | order | ||||
– | – | – | ||||
1.9172 | 1.9130 | 1.9139 | ||||
1.9580 | 1.9560 | 1.9560 | ||||
1.9788 | 1.9772 | 1.9779 |
order | order | order | ||||
– | – | – | ||||
1.9172 | 1.9130 | 1.9139 | ||||
1.9580 | 1.9560 | 1.9560 | ||||
1.9788 | 1.9772 | 1.9779 |