Matter is composed of atoms separated by empty space through which the atoms move...
Why isn't there an article before the words "empty space"?
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By not using an article, the author is referring to a general
which is what is between all matter.
the empty space
would refer to a specific empty space.
The empty space between atoms...
The US and Europe are separated by the Atlantic Ocean.
an empty space
Matter is composed of atoms separated by an empty space
would make the empty space more specific in relation to the atoms
The US and Europe are separated by an ocean.
in this case ocean is associated by its relationship to the US and Europe.
The US is separated from Europe and Japan by ocean.
in this case it is the generic ocean that is being referred to.
It also helps that empty space is noncountable.