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<p>Johns Hopkins checks all of your boxes (strong math and science, northeast, 5000 undergrads, flexible curriculum). They are very holistic in their admissions and ignore freshman grades, but for RD it would probably still be a reach for you. Just not as much of a reach as UChicago, MIT, Brown, or Stanford.</p>
<p>Tufts is another good option, not quite as strong in math and science, but it would also be a reach (similar to JHU). </p>
<p>I’m not very familiar with Amherst or Colgate.</p>