The Perron-Frobenius theorem is about the largest eigenvalue and eigenvector of a non-negative (irreducible) matrix.
My question: Is there any estimation of the difference between the first and second largest eigenvalues, say an upper or a lower bound?
An general theory may be tough, so please feel free to add other conditions to limit our discussion.
There certainly isn't a useful one. Consider the matrices
$$A_\lambda=\left(\begin{array}{cc} \tfrac{1+\lambda} 2&\tfrac{1-\lambda} 2 \\ \tfrac{1-\lambda} 2 & \tfrac{1+\lambda} 2\end{array}\right)$$ for $\lambda\in(0,1)$
Then $A_\lambda$ is irreducible and has eigenvalues $1$ and $\lambda$.
For an irreducible Markov chain the second eigenvalue represents the rate that the chain converges to its invariant distribution. This can be incredible fast, or incredibly slow.