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Two years ago, I applied to PhD programs (in Physics, if it matters); my undergrad was characterized mostly by underachievement, so my application was pretty weak (poor GPA, generic LORs, no research experience, etc.) Understandably, I did not get the response I was hoping for, and I decided to go for my Master's, both to put myself in a better position and to make sure academia is really what I wanted.

Fast forward two years and I'm in a bit of an awkward spot; I've done well in my Master's and I want to apply to PhD programs, but I'm not sure how to characterize my less-than-traditional path (it is relatively uncommon, at least stateside, to attend a terminal master's program in Physics). All aspects of my application are much better on paper (research, GPA, recommendations; except my GRE scores, which were already quite strong), but I'm worried about coming off as a second-rate student who couldn't make it the first time. Even my advisor, who thinks my application is otherwise quite strong, said he's unsure how it will be received.

Many of the schools I'm applying to are ones I applied to previously. Should I emphasize the upward trend through my Master's and how I've improved since my previous applications? Or is it not even worth mentioning (I could always use the extra space to talk about research) or possibly harmful?

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    How did previous students from the program do? If the program is a known quantity it should be fine. That guarantees nothing, but it sounds like you accomplished the goal at your current program. – Jon Custer Oct 14 '16 at 21:25
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    That is a good question, and one I really should have looked at more closely before I entered. I know many have continued on to a PhD at the same institution (it really is a great school), but I get the feeling few continue on towards a PhD elsewhere. I'm unsure if that's because they are unable or don't want to; I suppose I'll ask around more. – sabreitweiser Oct 14 '16 at 21:38
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    Chances are the admissions people may not even remember that you applied previously. Keep in mind that recent performance gets more weight. Make sure to apply to a "safety" school that might not be your heart's desire but that you would still find rewarding. – aparente001 Oct 14 '16 at 22:55
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Your masters program experience will likely give you a boost if it will make your letters less generic and you can demonstrate research experience. It's possible some programs will not think you worthy, I don't know how self-absorbed those programs are in physics, but in biology a commitment and talent for research are prized above classroom performance.

I wouldn't stress so much your former poor application and instead focus on your recent successes, and use your personal statement/whatever equivalent is available to make clear your goals, and you could also use that space to reference your goals for your masters. Paraphrased, "In my masters program I set out to accomplish _______. Now I would like to continue/add to/expand towards ________."

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