Undergraduate research in graduate school admission

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If I did theoretical research in a certain area of physics but applied to graduate school indicating interest in another area of theory, will that affect my chances?
 
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Very unlikely it will hurt you at all. You don't get accepted to graduate school because you are an expert in an area already.
 
Indeed, the point of undergraduate research is less the actual findings of the research and more the process. Of course, it's nice if you go into graduate school already having familiarity with a particular subfield, but certainly not necessary. The main point is to show that you're a competent researcher, and that you enjoy it enough to commit to several years of full time research. With that it mind, it's clear that the particular field of research is not so relevant.