How much does this novel have to do with calculus? Well in one way it has nothing to do with the real mathematical principles, but actually, calculus can be viewed in this novel as a thematic symbol, pointing to the strange order of reality and the human duty to science and exploration. For Newton's contribution, that he simultaneously discovered calculus alongside Leibnitz, another super-genius, is enough for the novelist to award him a sacred literary rite: The literary resurrection from the dead using the legendary alchemical "Philosopher's Stone."
The Philosopher's Stone is a symbol of transformation between lead and gold, and it symbolizes the ability to attain immortality in the soul. So the novelist's employment of this alchemical theme is another way of saying that because of Newton's philosophical contribution, he is immortalized (that, by calculus, he explained more about the universe and it's laws of nature). Because the novel remembers other historical characters, there is a legendary quality to these historical changes.
Another important literary feature of the book is the man who prints fake money runs away with the handmaiden of the Princess, Jack the Coiner. Jack the Coiner's initials are JC, which is a subtle reminder of Jesus Christ, and because of Jack's duplicity, he is kind of an anti-Christ figure, and so when his girlfriend and he escape to Louis XIV, there is a subtle allusion to the book of Revelation and the passage of the beast and the harlot. In any case, the novel definitely plays on religious themes, pointing not to the church but to science as the true standard for human reason.