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I tried to calculate the effect of spin orbit coupling $H_s=\alpha(\sigma_xp_y-\sigma_yp_x)$ as in the Rashba effect.

But I just found out that it is not hermitian. Some paper propose some way by adding the hermitian conjugate to ensure the hermicity.

However, when I tried to add a h.c. term, the Hamiltonian turned out to be 0.

$H_s=\alpha(\sigma_xp_y-\sigma_yp_x)=\alpha\left( \begin{array}{cccc} 0&\frac{\hbar}{i}\frac{\partial}{\partial y}+\hbar\frac{\partial}{\partial x}\\\frac{\hbar}{i}\frac{\partial}{\partial y}-\hbar\frac{\partial}{\partial x}&0 \end{array}\right)$

This matrix is just anti-hermitian and will end up to be 0 after adding up its hermit conjugate. Am I doing this correctly?

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The momentum and spin operators do commute. Since $H_s$ is a sum of products of commuting Hermitian operators, it is Hermitian (assuming $\alpha$ is real).

The matrix you have written to represent $H_s$ is correct and Hermitian. But you're right that it appears to be anti-Hermitian. To see what's wrong, consider the simpler $1\times 1$ matrix $$ \frac{\hbar}i \frac{\partial}{\partial x} $$ This looks anti-Hermitian too, since taking the conjugate transpose seems to give the same thing back with a minus sign. But of course we know this thing is really Hermitian because it's the operator representing $x$-momentum, which is an observable.

Here's what we've been missing. $\frac{\partial}{\partial x}$ is not just a number. It's an operator that acts on states and returns different states. When we do the Hermitian conjugate we have to remember to take the transpose of this operator. And the transpose of $\frac{\partial}{\partial x}$ is in fact $-\frac{\partial}{\partial x}$. To see this, let $|\psi\rangle$ and $|\psi'\rangle$ be any two states, with wavefunctions $\psi$, $\psi'$. The transpose of $\frac{\partial}{\partial x}$ is defined by $$ \langle{\psi'}|\left(\frac{\partial}{\partial x}\right)^T|\psi\rangle =\langle{\psi}|\left(\frac{\partial}{\partial x}\right)|\psi'\rangle^* $$ We can write the right hand side in terms of the wavefunctions like so: $$ \langle{\psi'}|\left(\frac{\partial}{\partial x}\right)^T|\psi\rangle =\int dx \psi(x)\frac{\partial}{\partial x}\psi'^*(x) $$ Integrating this by parts gives $$ \langle{\psi'}|\left(\frac{\partial}{\partial x}\right)^T|\psi\rangle =-\int dx \psi'^*(x)\frac{\partial}{\partial x}\psi(x) $$ which, translated back into bras and kets, reads $$ \langle{\psi'}|\left(\frac{\partial}{\partial x}\right)^T|\psi\rangle =-\langle{\psi'}|\left(\frac{\partial}{\partial x}\right)|\psi\rangle. $$ So since the states were arbitrary $$ \left(\frac{\partial}{\partial x}\right)^T = -\left(\frac{\partial}{\partial x}\right). $$

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