Indefinite article with substances

To some extent this may be a case of the accepted usage in the field in question, which I assume is chemistry, or perhaps physics.

I say this because, just based on my ordinary understanding of the noun, "optically thin gas," I would say you do in fact need the indefinite article ("an") in both of your examples. And I would say that, if you take out the "an," you want to make "gas" plural ("gases").

So what I'm saying is, based on my non-specialist understanding of what these sentences say, you would always want to say "a" or "the" with the singular ("optically thin gas") and omit the article with the plural ("optically thin gases").

Another way of putting this is that it depends on whether, in your field or context, "gas" is being used an a countable or uncountable noun. If it's a countable noun, then you'd want to use an article with the singular, and no article with the plural. If it's an uncountable noun, you would omit the article in the singular. Sometimes nouns can be both countable and uncountable, with subtle differences in meaning. If this is a case like that, then when you use the article, you are referring to the countable noun (a specific gas, one of many gases that can be counted). When you omit the article, you are referring to the uncountable noun (gas in general, like "love" or "money" or "truth" or "beauty" or "justice").

Having looked up 'optically thin gas' and 'optical depth' I find that the terms relate to astrophysics and the optical properties of the atmospheres of planets, photospheres of stars and, possibly, clouds of interstellar gas.

As most of these phenomena are mixtures of different gases (our own atmosphere consists of Nitrogen, Oxygen, Carbon Dioxide, Hydrogen and so on) and are often of unknown composition I suggest that using the uncountable form of the noun (without an indefinite article) is more appropriate since 'an optically thin gas' would imply purity of the gas and knowledge of its composition (it is appropriate to refer to "an inert gas" for example).

It would be appropriate to use the definite article if you were talking about a specific accumulation of optically thin gas which had been previously defined (such as the photosphere of a particular star) but not the indefinite article when discussing optically thin gas in general.