Question 11.14: A biological medium consists of two substances 1 and 2 of de...

A biological medium consists of two substances 1 and 2 of densities n_1 and n_2 . This medium is generating both substances by processes characterised by the matter source densities π_1 (n_1, n_2) and π_2 (n_1, n_2) . The substances 1 and 2 can diffuse inside this medium. The matter current densities j_1 and j_2 follow Fick’s law (11.51),

j_A = −D(s, μ_A) ∇n_A                       (11.51)

j_1 = −D_1∇ n_1         and        j_2 = −D_2∇ n_2

At equilibrium, the system is assumed to be homogeneous and characterised by the densities n_{01} and n_{02} of substances 1 and 2. In the neighbourhood of the equilibrium, the matter source densities π_1 (n_1, n_2) and π_2 (n_1, n_2) are given to first-order in terms of the density perturbations Δn_1 = n_1 − n_{01} and Δn_2 = n_2 − n_{02} by,

π_1 (n_1, n_2) = Ω_{11} Δn_1 +Ω_{12} Δn_2

 

π_2 (n_1, n_2) = Ω_{21} Δn_1 +Ω_{22} Δn_2

where the coefficients Ω_{11}, Ω_{12}, Ω_{21}, Ω_{22} are given by,

Ω_{11} = \frac{∂π_1}{∂n_1}                           Ω_{12} = \frac{∂π_1}{∂n_2}

 

Ω_{21} = \frac{∂π_2}{∂n_1}                         Ω_{22} = \frac{∂π_2}{∂n_2}

Assume that the processes to generate substances 1 and 2 are the two chemical reactions 1 \xrightarrow{α} 2  and 2 \xrightarrow{b} 1 described by the stoichiometric coefficients ν_{α1} = −1, ν_{α2} = 1, ν_{b1} = 1, ν_{b2} = −1 and the reaction rate densities ωα and ωb. Assume that the temperature T and the chemical potentials μ_1 and μ_2 are homogeneous, i.e. ∇T = 0 and ∇μ_1 = ∇μ_2 = 0 . Analyse the evolution of the density perturbations Δn_1 and Δn_2 by using the following instructions :
a) Express the coefficients Ω_{11}, Ω_{12}, Ω_{21}, Ω_{22} in terms of the total density n = n_1 + n_2 , the density perturbations Δn_1 and Δn_2 , the temperature T and a scalar W ≥ 0, which is
a linear combination of Onsager matrix elements L_{αα}, L_{αb}, L_{bα} and L_{bb} . Begin by using the second law, i.e. π_s ≥ 0 , and the relation (8.68) for a mixture of ideal gas.

μ_A (T, p, c_A) = μ_A (T, p) + RT \ln (c_A)                  (8.68)
b) Determine the coupled time evolution equations for the density perturbations Δn_1 and Δn_2 .
c) Show that under the condition imposed in a) the relation,

\Biggl(\begin{matrix} Δn_1 (t) \\ Δn_2 (t) \end{matrix} \Biggr) = e^{\lambda t} \cos (k.r+\varphi ) \Biggl(\begin{matrix} Δn_1 (0) \\ Δn_2 (0) \end{matrix} \Biggr)

is a solution of the coupled time evolution equations with λ < 0.

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a) Using the definition (10.25) for the matter source densities π_1 (n_1, n_2) and π_2 (n_1, n_2) for the stoichiometric coefficients ν_{α1} = −1, ν_{α2} = 1, ν_{b1} = 1, ν_{b2} = −1 , we can write that,

\pi _A = \sum\limits_{\alpha =1}^{n}{\omega _\alpha } \nu _{\alpha A}        (10.25)

  π_1 (n_1, n_2) = Ω_{11} Δn_1 +Ω_{12} Δn_2 = ν_{α1} ω_α + ν_{b1} ω_b = −(ω_α − ω_b)

 

π_2 (n_1, n_2) = Ω_{21} Δn_1 +Ω_{22} Δn_2 = ν_{α2} ω_α + ν_{b2} ω_b = ω_α − ω_b

Using the definition (8.18) for the chemical affinities A_α  and A_b ,

A_\alpha = -\sum\limits_{A=1}^{r}{\mu _A}\nu _{\alpha A}       (8.18)

A_α = −μ_1 ν_{α1} − μ_2 ν_{α2} = μ_1 − μ_2

 

A_b = −μ_1 ν_{b1} − μ_2 ν_{b2} = −(μ_1 − μ_2) = −A_α

Since there is no expansion of the system, i.e. ∇ · ν = 0, the scalar linear empirical relations (11.6) reduce to,

\begin{cases}\omega _\alpha = \sum\limits_{b=1}^{n}{L_{\alpha b} A_b + L_{\alpha f} \nabla .\nu } & \forall \alpha =1,….,n \\ \tau ^{fr} = \sum\limits_{b=1}^{n}{L_{fb}A_b + L_{ff} \nabla .\nu } \end{cases}     (11.6)

ω_α = L_{αα} A_α + L_{αb} A_b = (L_{αα} − L_{αb})A_α = (L_{αα} − L_{αb}) (μ_1 − μ_2)

 

ω_b = L_{bα} A_α + L_{bb} A_b = (L_{bα} − L_{bb})A_α = (L_{bα} − L_{bb}) (μ_1 − μ_2)

Since the temperature and the chemical potentials are homogeneous, i.e. ∇ T = 0 and ∇μ_1 = ∇μ_2 = 0 , the second law (10.88) reduces to,

\pi _s = \frac{1}{T} \left\{\sum\limits_{\alpha =1}^{n}{\omega _\alpha }A_\alpha +\tau ^{fr}(\nabla .\nu ) + j_s .(-\nabla T ) + \sum\limits_{A=1}^{r}{j_A} .(-\nabla \mu _A -q_A \nabla \varphi ) \right\}           (10.88)

\pi _s = \frac{1}{T} (ω_α A_α + ω_b A_b) = \frac{A_α}{T}(ω_α − ω_b) = \frac{A^2_α}{T} (L_{αα} − L_{αb} − L_{bα} + L_{bb}) = \frac{ W A^2_α}{T}≥ 0

which implies that W ≥ 0 since T > 0 and A^2_α≥ 0 . Thus,

Ω_{11} Δn_1 +Ω_{12} Δn_2 = −(ω_α − ω_b) = −W(μ_1 − μ_2)

 

Ω_{21} Δn_1 +Ω_{22} Δn_2 = ω_α − ω_b = W(μ_1 − μ_2)

Now, we have to express the chemical potentials μ_1 and μ_2 in terms of the concentration n_1/n and n_2/n of substances 1 and 2 using the relation (8.68) for a mixture of ideal gases,

μ_A (T, p, c_A) = μ_A (T, p) + RT \ln (c_A)                  (8.68)

\mu _1(T,n_1,n) = \mu _1(t,n_1 )+ R T\ln \bigl(\frac{n_1}{n}\bigr) = μ_1 (T, n_1) + R T \ln \Bigl(\frac{n_{01}+\Delta n_1}{n}\Bigr)

 

\mu _2(T,n_2,n) = \mu _2(t,n_2 )+ R T\ln \bigl(\frac{n_2}{n}\bigr) = μ_2 (T, n_2) + R T \ln \Bigl(\frac{n_{02}+\Delta n_2}{n}\Bigr)

which can be recast as,

μ_1 (T, n_1, n) = μ^0_1 (T, n_1, n) + R T \ln \Bigl(1+\frac{\Delta n_1}{n}\Bigr)

 

μ_2 (T, n_2, n) = μ^0_2 (T, n_1, n) + R T \ln \Bigl(1+\frac{\Delta n_2}{n}\Bigr)

where the chemical potentials at equilibrium are,

μ^0_1 (T, n_1, n) = μ_1 (T, n_1) + R T \ln (\frac{n_{01}}{n}\bigr)

 

μ^0_2 (T, n_2, n) = μ_2 (T, n_2) + R T \ln (\frac{n_{02}}{n}\bigr)

At equilibrium the chemical potentials are equal,

μ^0_1 = (T, n_1, n) = μ^0_2 =(T, n_2, n) ≡ μ^0 (T, n_1, n_2)

Thus, for small density perturbations, i.e. Δn_1 \ll 1 and Δn_2 \ll 1 , the chemical potentials become,

μ_1 (T, n_1, n) = μ^0 (T, n_1, n_2) + R T \frac{Δn_1}{n}

 

μ_2 (T, n_1, n) = μ^0 (T, n_1, n_2) + R T \frac{Δn_2}{n}

Hence,

Ω_{11} Δn_1 +Ω_{12}Δn_2 = −W(μ_1 − μ_2) = − \frac{R T W}{n} (Δ n_1 − Δn_2)

 

Ω_{21} Δn_1 +Ω_{22}Δn_2 = W(μ_1 − μ_2) =  \frac{R T W}{n} (Δ n_1 − Δn_2)

which implies that the coefficients are given by,

Ω_{11} = Ω_{22} = −\frac{R T W}{n} ≤0       and        Ω_{12} = Ω_{21} = \frac{R T W}{n}≥0

b) Using the matter current densities j_1 and j_2 , the matter continuity equations can be recast as,

\dot{n}_1 = D_1∇^2 n_1 + π_1 (n_1, n_2)        and        \dot{n}_2 = D_2∇^2 n_2 + π_2 (n_1, n_2)

where the Laplacian ∇^2 = ∇ · ∇ is a scalar operator. Introducing the scalar Ω ≡ Ω_{12} = Ω_{21} = −Ω_{11} = −Ω_{22} ≥ 0 and using the relations for the matter source densities π_1 (n_1, n_2) and π_2 (n_1, n_2) , the matter continuity equations become,

\dot{n}_1 =  D_1∇^2 n_1 − Ω Δn_1 + Ω Δn_2 .

 

\dot{n}_2 =  D_2∇^2 n_2 + Ω Δn_1 – Ω Δn_2 .

Since Δn_1 = n_1 − n_{01} and Δn_2 = n_2 − n_{02} where n_{01} and n_{02} are constants,

\dot{n}_1 = Δ\dot{n}_1               \dot{n}_2 = Δ\dot{n}_2   ∇^2 n_1 = ∇^2 (Δn_1)                   ∇^2 n_2 = ∇^2 (Δn_2)

Thus, the coupled time evolution equations for the density perturbations Δn_1 and Δn_2 yield,

\dot{n}_1 = D_1∇^2 (Δn_1) − Ω Δn_1 + Ω Δn_2

 

\dot{n}_2 = D_2∇^2 (Δn_2) +Ω Δn_1 – Ω Δn_2

c) The coupled time evolution equations can be written as a matrix system,

\Biggl(\begin{matrix} \Delta \dot{n}_1 \\ \Delta \dot{n}_2 \end{matrix} \Biggr) = \Biggl(\begin{matrix} -\Omega +D_1\nabla^2 & \Omega \\ \Omega & -\Omega +D_2\nabla^2 \end{matrix} \Biggr) \Biggl(\begin{matrix} \Delta n_1 \\ \Delta n_2 \end{matrix} \Biggr)

Replacing the solution in the coupled time evolution equations and then using the relations,

\dot{n}_1 = λΔn_1      and      ∇^2 (Δn_1) = −k^2 Δn_1

 

\dot{n}_2 = λΔn_2      and      ∇^2 (Δn_2) = −k^2 Δn_2

the matrix system can be recast as,

\Biggl(\begin{matrix} -\Omega -D_1k^2-\lambda & \Omega \\ \Omega & -\Omega -D_2k^2 -\lambda \end{matrix} \Biggr) \Biggl(\begin{matrix} Δn_1 \\ Δn_2 \end{matrix} \Biggr)=0

For non-trivial solutions, the determinant of this matrix vanishes,

(Ω+D_1 k^2 + λ)(Ω+D_2 k^2 + λ)− Ω^2 = 0

which is recast as,

λ^2 + 2 ω λ + α = 0

where,

ω ≡ \frac{1}{2}\Bigl(2\Omega +(D_1+D_2)k^2\Bigr)\geq 0

 

α ≡(Ω+D_1 k^2)(Ω+D_2 k^2)− Ω^2 ≥ 0

which implies that ω^2 − α ≥ 0 . The solutions of the quadratic equation in λ are,

\lambda _1= – \omega +\sqrt{\omega ^2-\alpha }

 

\lambda _2= – \omega -\sqrt{\omega ^2-\alpha }

These solutions are called the Lyapunov exponents of the system. Under the assumption of a closed system undergoing chemical reactions transforming substance 1 into substance 2 and vice versa, the Lyapunov exponents are negative, i.e. λ_1 < 0 and λ_2 < 0 , which corresponds to stable solutions. For the formation of instabilities, where the density perturbations grow exponentially, at least one of the Lyapunov exponents has to be positive, i.e. λ_1 > 0 or λ_2 > 0 . Thus, in a closed system, density perturbations cannot grow. In order to see the rise and growth of instabilities, which can lead to the formation of patterns called Turing patterns, there has to be a source for the substances 1 and 2, which is the environment.

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