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As the title suggests, I know collision of galaxies happens. Questions are

  1. Why do they collide (obviously because of gravity, but in what conditions)?
  2. Aftermath of the collision?
  3. If there is a super massive blackhole in the center of the galaxies, what happen to them?
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2 Answers

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Galaxies collide due to gravatational entanglement, same as more solid objects, as well as simple trajectory bringing them close enough to interact. Andromeda and the Milky Way are likely to collide, or possibly graze close enough for some interaction, sometime in the 2-5 billion year range (opinions vary), so we're going to get a close view of such a thing.

Once two galaxies start to interact, much less outright collide, it does cause stars to shift in their galactic orbits. Perfect spirals become elongated spirals, or the galactic disk warps. A tail of stars begins to form between them as stars, disrupted in their orbits, follow new paths that can lead to stars orbiting a new galaxy, or perhaps thrown off into space all together. This 'tidal tail' is a good clue that a galaxy is currently, or recently has undergone either collision or interaction.

Once the interaction gets closer, the actual collision, it tends to get very bright. The interstellar gas of both galaxies merge with each other, but with differential speeds, which creates eddies and in turn triggers star formation. Actively colliding galaxies are bright with new stars. Interactions with the stars of both galaxies is complex and can definitely throw stars into new orbital trajectories, if not sling-shot right out of the merging galaxies all together.

The form the newly merged galaxies take depends a lot on the sizes of the encountering galaxies and the differential thereof. Dwarf galaxies interacting with large spirals may not do much to the spiral, but two spirals of equivalent size interacting should cause massive disruption of both.

Sometimes a merger is not fully accomplished on the first pass, and a much reduced core of one of the galaxies will emerge from the other side (presumably with the black hole intact), which may continue onwards, or may not escape interaction and circle back for another go some time later. The Omega Centauri cluster, presumed to be in orbit around the Milky Way, just might be such a remnant.

As for the black-holes current models suggest that at least their first contact is likely to cause one of them to recoil as differential rotation is translated into angular velocity, which should cause gravity waves and definitely cause an X-ray flare that should be visible to the right instruments. Mergers of such supermassive black holes are thought to occur, though I don't recall what that would look like to observatories here on Earth.

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I really like the way we talk about events that will occurr in billions of years as if we are going to be alive to witness the events. –  Paulo Santos Jun 12 '11 at 13:43
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It takes millions of years for galaxies to collide so even though they're mainly gas and dust they have a weak force of attraction. Also as you mentioned in your question they have a super massive black hole in the middle that pulls them together and drags the rest of the galaxy with them.

It's also incredibly unlikely that even one of the stars will collide with each other because of the huge amount of space between every star, even though when you look at a galaxy it appears as a blur.

Eventually after the galaxies have collided they spiral into one, they look a bit mishapen but eventually they become one galaxy, here is the Antennae Galaxy that has recently (in astronomical terms) collided:

The Antennae Galaxy

When the black holes collide I doubt anything special would happen, I think it would just merge into a larger one because whichever black hole is stronger would pull the other inside it and just increase it's mass and strength.

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Thanks for the image –  user Jun 11 '11 at 10:57
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Galaxies aren't mostly gas and dust. Most of their mass is contained in dark matter. Furthermore, most of the luminous mass is contained in stars. –  voithos Jun 12 '11 at 3:56
    
Well no but really a star is the same as a spec of dust at this scale but yes i know it's not really just gas and dust. –  Cameron Jun 12 '11 at 15:51
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@Cameron: The funny thing is that, as you said, although the stars themselves don't interact much (except gravitationally) during the collision, the gas and dust do interact, and sometimes form such "starburst" regions, like the Antennae Galaxy which you referenced. –  voithos Jun 14 '11 at 20:44
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As an undergrad, I was assigned to calculate the average number of direct star collisions expected for galaxies undergoing a collision. The answer? One. Not a "microscopic probability of it ever happening at all", and not "a huge, huge number," which are usually the only two answers you ever get for that flavor of astronomical question. ONE. –  Andrew Jun 23 '11 at 18:14
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