Analysis of top-swap shuffling for genome rearrangements (Q2467609)

A top-swap Markov chain is described which can be considered as a card-shuffling process. It is used to model reciprocal translocations between chromosomes. The model has two parameters: the number of genes (cards) \(n\) and the number of chromosomes (decks) \(k\). The cards are ordered in each deck. At each transition two random positions are chosen at decks and if they are in different decks the tops of these decks are exchanged. If the positions are at the same deck there are two variants: to do nothing or to invert the order of cards between these positions. (The last variant is used to describe genes inversion). Let \(\tau(n,k)\) be the relaxation time (the inverse of the spectral gap) of the top-swap chain. It is shown that \(\exists\;C_1>C_2>0\) such that \[ C_1(n+k)\leq \tau(n,k)\leq C_2(n+k). \] Some generalizations are also considered.