As is well known, coordinates of D-branes are described by NxN matrices. From
generic non-commuting matrices, it is difficult to extract physics, for
example, the shape of the distribution of positions of D-branes. To overcome
this problem, we generalize and elaborate on a simple prescription, first
introduced by Hotta, Nishimura and Tsuchiya, which determines the most
appropriate gauge to make the separation between diagonal components (D-brane
positions) and off-diagonal components. This prescription makes it possible to
extract the distribution of D-branes directly from matrices. We verify the
power of it by applying it to Monte-Carlo simulations for various lower
dimensional Yang-Mills matrix models. In particular, we detect the topology
change of the D-brane bound state for a phase transition of a matrix model; the
existence of this phase transition is expected from the gauge/gravity duality,
and the pattern of the topology change is strikingly similar to the counterpart
in the gravity side, the black hole/black string transition. We also propose a
criterion, based on the behavior of the off-diagonal components, which
determines when our prescription gives a sensible definition of D-brane
positions. We provide numerical evidence that our criterion is satisfied for
the typical distance between D-branes. For a supersymmetric model, positions of
D-branes can be defined even at a shorter distance scale. The behavior of
off-diagonal elements found in this analysis gives some support for previous
studies of D-brane bound states.Comment: 29 pages, 16 figure