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The function representation of this system's Hamiltonian will look like:
$$H=-\frac{\hbar^{2}}{2m}\frac{\partial^{2}}{\partial x^{2}} + V_{atom}\left(x-a\right) + V_{atom}\left(x-2a\right) \; \; . $$
Our goal: Find the eigenstates $\vert \psi_{n} \rangle$ of this system's Hamiltonian $H$, and find the eigenenergy of each state.
$$\vert 1 \rangle \; \dot{=} \; \phi^{g}(x-a) \; \; $$
and
$$\vert 2 \rangle \; \dot{=} \; \phi^{g} (x-2a) \; \; .$$
Notice that the basis wave functions are now centered at their respective atoms. Working in the ground state basis, the eigenstates must have the form
$$\vert \psi \rangle \; = \; c_{1} \vert 1 \rangle + c_{2} \vert 2 \rangle \; \; . $$
$$H \, \vert \psi_{n} \rangle \; = \; E_{n} \, \vert \psi_{n} \rangle \; \; .$$
$$H \; = \; \left[\begin{array}{cc} \alpha & \beta \\ \beta & \alpha \\ \end{array}\right] \; \; . $$
NOTE: If students are puzzled by why you chose this form, remind them that the Hamiltonian is an observable. Because of this, the matrix must be Hermitian.
Alternatively, the Hermitian matrix can also be represented as
$$H \; = \; \left[\begin{array}{cc} \langle 1 \vert H \vert 1 \rangle & \langle 1 \vert H \vert 2 \rangle \\ \langle 2 \vert H \vert 1 \rangle & \langle 2 \vert H \vert 2 \rangle \\ \end{array}\right] \; \; , $$
where
$$\alpha=H_{11}=H_{22}=\langle 1 \vert H \vert 1 \rangle=\langle 2 \vert H \vert 2 \rangle \; \; ,$$ $$\beta=H_{12}=H_{21}=\langle 1 \vert H \vert 2 \rangle=\langle 2 \vert H \vert 1 \rangle \; \; .$$
Notice that $\alpha$ is just computing the expectation value for either the first or second basis state, while $\beta$ is called an overlap evaluation. For the two-well system, $\beta$ is actually a negative value associated with the probability of an electron to move between wells.
If you choose, this is a good opportunity to discuss solving for $\alpha$ and $\beta$.
NOTE: If students are puzzled by the Hamiltonian representations, remind them that $\vert 1 \rangle$ and $\vert 2 \rangle$ are the basis states, and can be represented in matrix notation as
$$\vert 1 \rangle \; \dot{=} \; \left[\begin{array}{c} 1\\ 0\\ \end{array}\right] \; \; \; \; \; \; \; \text{and} \; \; \; \; \; \; \; \vert 2 \rangle \; \dot{=} \; \left[\begin{array}{c} 0\\ 1\\ \end{array}\right] \; \; . $$
Performing the matrix operations will show that
$$\langle 1 \vert H \vert 1 \rangle = \left[\begin{array}{cc} 1 & 0 \\ \end{array}\right] \left[\begin{array}{cc} \alpha & \beta \\ \beta & \alpha \\ \end{array}\right] \left[\begin{array}{c} 1\\ 0\\ \end{array}\right] = \alpha \; \; . $$
$$\vert \psi_{1} \rangle \; \dot{=} \; \left[\begin{array}{c} 1\\ 1\\ \end{array}\right] \; \dot{=} \; \vert 1 \rangle + \vert 2 \rangle \; \; \; \; \; \; and \; \; \; \; \; \; E_{1}=\alpha+\beta \; \; ,$$
while
$$\vert \psi_{2} \rangle \; \dot{=} \; \left[\begin{array}{c} 1\\ -1\\ \end{array}\right] \; \dot{=} \; \vert 1 \rangle - \vert 2 \rangle \; \; \; \; \; \; and \; \; \; \; \; \; E_{2}=\alpha-\beta \; \; .$$
Ask the class if these states are properly normalized. How would they properly normalize the eigenstates?
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Does this look familiar? Graphically representing the eigenstates yields envelope functions nearly identical to those we saw in the coupled oscillator. This motivates us to introduce envelope functions to make a function representation of our final wave states.
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The function representation of each eigenstate is equivalent to the bra-ket notation, but now we can explicitly show how the wave vector of the envelope function and location of the well will affect each coefficient in the eigenstates.