There's nothing here which is unique to scientific models or theories. With one exception, the examples you have provided are simply compound nouns which require the definite article when they are placed in a position in a sentence which requires an article.
The exception is "The Newton's theory" - which is plain wrong. I'm not sure where you read this. Newton is the name of a man, and you do not apply articles to people's names. You would simply say "Newton's theory"; "The theory of Newton", or, if you wanted something close to your own quote, "The man's theory" (where the man was Newton).
Example requiring an article:
- I first read about the multiverse theory when I was 15.
Example not requiring an article:
- Multiverse-theory adherents tend to have an interest in science.
There's nothing unique in this usage which is applied especially to scientific concepts. You could substitute any other similar compound nouns in their place.