Solving 2nd Order PDE System with Crank-Nicholson

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I have the following system of PDEs:
[tex] \hat{\rho}\hat{c}_{th}\frac{\partial\hat{T}}{\partial\hat{x}}-\alpha_{1}\frac{\partial}{\partial\hat{x}}\left(\hat{k}(\hat{x})\frac{\partial\hat{T}}{\partial\hat{x}}\right)=\alpha_{1}\hat{\sigma}(\hat{x})\hat{E}[/tex]
[tex] \frac{\partial}{\partial\hat{x}}(\hat{\varepsilon}(\hat{x})\hat{E})=-\beta\hat{c}[/tex]
[tex] \frac{\partial\hat{c}}{\partial\hat{t}}-\gamma_{1}\frac{\partial}{\partial\hat{x}}\left(\hat{D}(\hat{x})\frac{\partial\hat{c}}{\partial\hat{x}}\right)= \gamma_{2}\left(\frac{\partial\hat{E}}{\partial\hat{x}}+\frac{\partial\hat{c}}{\partial\hat{x}}-\frac{\partial\hat{T}}{\partial\hat{x}}\right)[/tex]

I would like to solve this system using the Crank-Nicholson method. Now for a linear equation, the CN scheme is well defined, MATLAB has some very nice algorithms for this.

However the first equation has a nonlinear term in E, and I have no equation which time steps E. I suppose that I could use a Newton-Raphson scheme to get the solution. Would that be the correct way forward?
 
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a perturbation expansion for [itex]E[/itex] (kill all the [itex]\hat{}[/itex], it makes the equations hard to read and is confusing, unless they are all vector quantities,l then you have a mess and an intractable system).