Will ISIS attacks hurt my PhD application as a Muslim?

Only indirectly.

Admissions committees have good incentive to get the sharpest, most hard working people into their programs. They will care about your excellent results, as they should.

But administrative procedures may hinder people coming from your part of the world more than other applicants. I am basing this on my experience of being a Serb who wanted to study at Western universities, while Serbia was screwing up royally on the political scene, waging wars and making enemies everywhere. Sanctions made it difficult to travel. A friend of mine was denied a visa even after being admitted into an academic program and obtaining funding. Tuition was more expensive for us (to study in the EU), but far less funding was available. Even though I obtained a scholarship that covered the tuition, it was paid to me in monthly installments while the university insisted that I (as opposed to EU students) pay the entire tuition up front. Nobody could employ me without massive administrative hassle, meaning I couldn't just work at a bar a few hours a week if I needed some extra cash. Phone companies would not let me have a contract with them, limiting me to expensive, pre-paid phone cards. And on and on the list goes.

So yes, I think your chances will be smaller, but not because of admissions committees within any given university. It could happen that academic staff are not sufficiently aware of the additional hurdles you're facing, though. On the other side of the equation, professors from your side of the world might be less experienced at writing recommendation letters, for example. So a number of small obstacles will accumulate, many of them stemming from recent and current world politics.

And my heart goes out to you. It sucks to be vilified by outsiders for things being done by people you don't identify with.

Will these events perhaps hurt my application?

No, I don't think you need to worry about this. It's possible in principle that they could, but only if something went terribly wrong. If I were on an admissions committee and detected any signs of religious or cultural bias along these lines, I would be shocked and would intervene, including getting the university administration involved if necessary. This form of prejudice is utterly unacceptable. Fortunately, it also seems to be rare in academia. I've never heard any of my colleagues say anything along these lines, while I've heard a number of them speaking out against such prejudice.

I'd be horrified if any department could put together an entire admissions committee in which bigots had real influence, and I don't think this is a realistic possibility. It's a little more worrisome in departments where individual faculty make admissions decisions. Academia is large enough that every field must contain at least a few bigots, so it's possible that you could send an application to such a person. I wouldn't worry about this, since bigotry is not at all common or accepted: I don't expect you'll run into it at all, and there's no way it could hurt many of your applications.

Will they? Yes. Is there anything you can do about it? Not much. Will it matter much? Hopefully not.

It is a fact of life that people are biased about almost everything all the time. Sometimes the biases are small sometimes they are big. That sucks, but it is human nature.

Usually people in most academic positions are able to overcome their silly biases and only rely on the ones that matter, like a bias toward good GPA.

What can you do about it? Exactly what you are doing: being a decent human being and excelling academically, this will hopefully move people's biases in a positive direction instead of the negative direction that well publicised attacks do.

Your academic profile is exceptionally strong — near-perfect GPA, 980 Physics GRE, 97th-percentile general GRE, and strong letters. In US graduate admissions, these metrics are the primary drivers of decisions. Faculty committees evaluate research potential, preparation, and fit with their programs. Your credentials place you competitively for top physics programs. Federal law (Title VI, Title VII) and university policies prohibit discrimination based on religion, national origin, or name. Admissions committees are trained to assess applications on merit. Thousands of students named Mohammed from the Middle East are admitted to US PhD programs every year. Your background does not diminish your qualifications. If anxiety persists, focus your energy on what committees actually weigh: a clear, specific research statement naming faculty whose work aligns with yours; a concise CV highlighting research experience; and, if offered, an optional diversity statement framing your perspective as an asset — not a liability. You do not need to address ISIS or terrorism; doing so distracts from your physics narrative. Practical step: email 2–3 faculty per target program before applying, attaching your CV and a one-paragraph research interest summary. Positive responses signal genuine fit. Your record speaks louder than any bias. Prepare thoroughly, apply broadly, and trust the process.