Does modern physics contradict transubstantiation?

There is quite a bit of literature on this subject. One approach is to admit that the Aristotelian categories adopted by the Church to describe transubstantiation do seem to contradict Newtonian physics, but Quantum physics has rendered the debate moot. Father Michael Kelly, the Jesuit CEO of the Asian Catholic news agency UCA News writes:

Regrettably, all too frequently, the only Presence focused on is Christ’s presence in the elements of bread and wine. Inadequately described as the change of the ‘substance’ (not the ‘accidents’) of bread and wine into the body and blood of Christ, the mystery of the real presence of Christ in the Eucharist carries the intellectual baggage of a physics no one accepts. Aristotelian physics makes such nice, however implausible and now unintelligible, distinctions. They are meaningless in the post-Newtonian world of quantum physics, which is the scientific context we live in today.

Deacon Steven D. Greydanus goes a step further:

A tesseract or wormhole warps space-time to bridge the distance between two locations that are far apart within four-dimensional space. The Eucharist does something similar, except that instead of two spatial locations, it bridges the infinite distance between Earth and Heaven; what it makes present is not the other side of the galaxy, but Christ in Heaven

However, Deacon Greydanus also warns:

Science reveals a world that exceeds the bounds of human experience, comprehension, and imagination. We cannot form an accurate imaginative picture of the world of quantum mechanics, any more than we can form an accurate imaginative picture of the body and blood of Christ being present under the appearances of bread and wine. Yet quantum theory allows us to make true statements about the unimaginable world of quantum physics and to avoid certain false ideas — and theology does something similar in regard to mysteries of faith.

In the end, for those who believe in the Real Presence, it is not a question of one contradicting each other. It has always been been a Mystery of Faith. On the other hand, who knows if the day is coming when Quantum physics well enable the faithful to "know," as well as to "believe."

A big cause for confusion is the traditional use of the words "substance" and "accident", whose common English meanings are opposite to how they are used when describing transubstantiation.

The official terms are:

• "substance": what is the essential quality of the object.
• "accident": what just happens to be an irrelevant attribute of the object.

Here, the word "substance" does not mean what the object is made out of. A better word would be "essence" (i.e. what is essential).

Consider that, after being transformed, what is essential is that the object is now a leg, a part of a table, and what is accident is that it happens to be made of wood. It would still be a leg even if it were made of plastic or metal.

Similarly in transubstantiation, after being transformed, what is essential is that the object is now part of Christ's body, and what is accident is that it happens to be made of bread.

Just as physics has nothing to say about the transformation of a tree into part of a table, it also has nothing to say about the transformation of a piece of bread into part of Christ.

Transubstantiation is entirely spiritual, not physical, so no laws of physics are involved.

NO, modern Physics restricts itself to the physical because it must. To say that that is all there is is to go beyond Physics. Transubstantiation is in no way a basis for Catholic teaching, but rather the opposite. It is showing that the Faith is not irrational by showing that it does not violate mainstream metaphysics.

The brilliant convert Catholic philosopher G E M Anscombe might put you at ease by this piece was written about her little child and the Eucharist https://archive.secondspring.co.uk/articles/anscombe.htm

Does modern physics contradict transubstantiation?

No. Why? Well, because...

According to modern physics, all physical things are reducible to atoms, and that's all they are.

...this is a philosophical assumption (commonly known as Philosophical Materialism) that cannot be proven scientifically. And, according to many Christians and even a number of scientists, it's wrong. Note that this assumption also a priori excludes God. Therefore, if God exists (and there is every reason to believe He does), then this assertion is false. Indeed, if consciousness cannot be reduced to material causes (as we have thus far failed to do), it is false.

So your question is based entirely on a specious assumption.

Noow, if your definition of "modern physics" is "materialism" (which, sadly, is the case for a great many "scientists"), then yes, it contradicts transubstantiation. But it does so by definition and by philosophy, not by evidence.