Thanks a lot for all your reply. I think I should clarify some points which will make it easier for you to analyze :
bfollinprm wrote:There also isn't really a safety in that list
I thought applying to a lot of good schools is just as good a strategy, my reasoning was something like this "I may not get into any particular school, but if I apply for lets say 10 schools, I'll get into one or the other". But in retrospect I don't think it was a good strategy. As for safety schools, I thought I had some in the list - namely UMich, UT Austin, Stony Brook, Rutgers - but in retrospect I think I was being overconfident and perhaps UMich & UT Austin wasn't a safety school for me after all. But do you honestly think that even Stony Brook wasn't a safety for me?
bfollinprm wrote:HEP-TH is very competitive
Do you mean some fields (like hep-th) are more competitive than others? Wow, somehow I didn't know that! Can you please explain why is it so?
TakeruK wrote:In addition, you are an international student, which makes it harder to get in, I think, since we cost more than domestic students!
I haven't thought about it earlier, but you are right for public universities (since there is the extra non-resident tuition part). But does it matter for private universities?
TakeruK wrote:I would first suspect things that aren't immediately obvious by this profile and/or things that are not quantifiable. The first non-quantifiable thing, but probably the most important in applications, is your LORs. I think it's very unusual for you to have submitted 6 LORs. I don't think that LORs "stack" -- instead they "average out". It sounds like some of your letters are definitely not as strong as others (i.e. the letters you submitted from graduate course instructors). I think 3 strong letters are much better than 3 strong letters + 3 mediocre letters (a "did well in class" letter is always mediocre). I guess it's also a possibility that your research letters were not as strong as you think they were. Getting a letter from a well known prof is only helpful if they are able to provide meaningful comments. Sometimes well-known/busy profs with big labs don't get to know their students as well and write more standard letters that aren't as helpful. I don't know the relationship you had with your letter writers, but the LORs might have been part of the result.
I didn't know '3 strong letters are much better than 3 strong letters + 3 mediocre letters', somehow I thought just the opposite and thats why I submitted as many recommendations as a grad school allows - may it be 3, 4 or 6; but now it looks like you are right. Only the 6th rec (when the grad school allows it) was a research recommendation, that too not in my field of interest (it was in astro), the 5th rec (when the grad school allows it) was from a professor (hep-ex) who knows me for years (initially as a student and later as grader), the top 4 (the ones from hep-th professors) were from graduate & advanced undergraduate classes (since I couldn't do research in hep-th). So you may be right, perhaps my recommendations weren't very stellar.
TakeruK wrote:The other non-quantifiable thing is your SOP / anything else you wrote in your application. Maybe you were not able to express your goals and research interests clearly enough to demonstrate a good fit with the department. I don't know if you were explaining all these details here on this post just for our benefit, but if you wrote about the same thing (or even more detailed) in your SOP, you might have been oversharing, in my opinion, for your application. Or maybe you didn't communicate it well and it sounds like you were trying to make excuses for things that don't really need excuses (or can't be excused). I'm also not sure why you felt you needed to attach a letter from your school's medical office to document your illness in your last year. If you still managed to get As in your last year, the letter is probably not necessary -- I would only think such a letter is necessary if you failed an entire year due to illness or had to take a break from school (but even so, just saying that you had medical issues is probably enough). Of course, perhaps you are not telling us everything here and maybe you had another good reason to include your medical letter, but I'm just going with the info I have here. In addition, you put your grad courses and "interesting undergrad courses" under "special bonus points" here. It's cool that you have grad courses but it usually won't make much of a difference in grad school admissions. I am not sure what's so interesting about the two undergrad courses you listed, either. So if you focused your SOP on the "wrong" things, that might have been a contributing factor. Things like your grad courses will show up on your transcript -- save your SOP space for research related things!
I was quite clear about my goals and research interests in my SOP. Almost all of the explanations & excuses here are for you guys to understand the situation better, I did not 'overshare' in my SOP. As I wrote earlier, due to illness I had to switch from focused option of Physics major to the flexible option, as a consequence of which I didn't have a senior thesis, which I thought was a big deal (infact the biggest weakness in my application in my opinion) and needed explanation -- I attached the letter from MIT Medical just to show that I wasn't making excuses. I thought completing graduate courses (including QFT & GR) demonstrates that I can handle graduate school (despite my low overall GPA); and those two undergraduate classes were among the factors that contributed to my decision of going for hep-th, which makes them 'interesting'. Again, I didn't make a big deal of it in my SOP; as you said, they are already in my transcript.
TakeruK wrote:Your grades in non-Physics courses might also be a flag! I agree that with your A's in later QM classes, the C in Quantum Physics 1 probably doesn't make a difference. The B in EM probably doesn't matter either. But I would raise an eyebrow at the C in Experimental Physics I (unless you got higher grades in later experimental courses) and because you said that your Math and Humanities classes lower your GPA significantly. I'm not sure what you mean by that exactly, but doing poorly in Math (you said As and Bs but what is the split?) isn't a good thing for a physicist (and I would actually count Math courses as part of a Physicist's "major GPA"). In addition, it sounds like you also did not do so well in the other sciences nor the Humanities. I don't think these things alone are a huge deal. However, when combined with your GRE scores, your profile demonstrates someone who is very proficient in coursework and theoretical physics, but you might not be a very well rounded person overall.
I didn't take any other experimental class, but why do you think it matters? Afterall, I'm going for hep-th, not hep-ex. By 'Humanities classes lowered my GPA significantly' I meant that while my grades in Physics courses were mostly A's (5.0/5.0), in other subjects I mostly received B's (4.0/5.0) - and there were quite a few of them, which brought my overall GPA close to 4.5/5.0 - significantly lower than my major GPA. I calculated my major GPA using only Physics courses (8.something), and I got 4.7/5.0, if I include Math courses (18.something) as well, it would be 4.6/5.0 instead - lower, but not too lower. Besides, are you sure B's are that bad at MIT? I don't know about others, but I had to work a lot to earn even those B's, so I wouldn't call it 'doing poorly'. I accept that I'm not a well rounded person, but I thought such things are relevant to college, not grad school. It may be my misconception, but I thought only Major GPA matters in case of grad school admissions, not overall GPA.
TakeruK wrote:Finally, maybe this is the most important part, and it ties all of the above together. I would strongly suspect that the main reason you did not get into these schools despite a strong profile (good grades and research experience) is probably due to a lack of fit. Related to what bfollinrpm said and point #2 above, you are applying to a very narrow research field and maybe the profs you wanted to work with did not have the resources to take you on, or that you did not clearly identify your interests / show a good enough fit for them to want to take you on. Maybe, since the field is so narrow, there were enough other people higher up on the list that got the spots instead. Your profile as presented here also shows that you are a "risky" student to take on. Sure, you might have great grades in Physics, but it's hard to say what your other skills (that are required for success in academia) are, especially with less than great performance outside something so narrow as Physics. I think your strange application (6 LORs, a medical letter etc.) and perhaps combined with a lack of demonstrated fit might have shown that you don't know what you were doing in your application and/or you don't know what you want to do in grad school. Again, this is only a guess -- I don't mean to offend! Overall, I think your goal might have been too narrow (in terms of the field and the calibre of schools you picked) so despite having a pretty good profile, the "narrowness" might have really raised the competition level!
Just to make it clear, I did not apply for String Theory only, that main & side thing in field of interest was a clarification for you guys, I applied for hep-th in general, although I did mention in my SOP that I'd be most interested in those 3 subfields - so it isn't as narrow as you make it sound like. And I'm pretty sure that I was quite clear about 'what I want to do in grad school' and why I'm interested in a particular graduate school (if thats what you mean by 'demonstrated fit') in my SOP. Also, can you please elucidate this -- "Your profile as presented here also shows that you are a "risky" student to take on. Sure, you might have great grades in Physics, but it's hard to say what your other skills (that are required for success in academia) are, especially with less than great performance outside something so narrow as Physics." -- because I didn't quite get the point.
TakeruK wrote:To answer your question, here are some things about your profile that might have contributed to the results. Of course, it's just my opinion -- people can't know for sure, but it's what you asked for

Also, I am purposely trying to pick out flaws (as you asked) so this post might be pretty negative, but I don't mean to put you down, just pointing out potential flaws.
Don't worry, I didn't take it personally. I know my application isn't flawless, and thats why I don't expect to get accepted at all of these schools, but from a neutral standpoint (i.e. not trying to pick up flaws only

) do you really think my application was so weak that I didn't have a chance of getting into even a single top 10 program, not even in 11-25 type programs?
TakeruK wrote:I think it's a good idea that you asked for feedback from the schools. I know some schools will do this but they generally wait until after the entire application season is over (e.g. May?) so ask again in a few months if you don't hear back from them! If you don't mind, you could post their response here, since it might help others. However, sometimes the responses aren't very helpful, and they might not tell you something like "your LORs were not so great" if they want to protect the LOR writers!
"While we are aware of difficulties beyond your control that you have had to endure during your studies, your course grades must be a part of our decision making process. Just to give you an example, you obtained a grade of C in Quantum Physics I - it is quite possible that this was due to ill health, and it is also possible that under ideal circumstances you may have obtained an A, but that is still a 'maybe', and this is a disadvantage compared to a competing application with straight A's. One other specific suggestion I can make is to further narrow down your area of research interest in your statement of purpose." -- UT Austin
"In your case I can say that HET is just incredibly competitive and all has to be pretty much perfect. It was deemed that it was not." -- UMich
"Since we will have an entirely new Admissions Committee for 2014-15, you may fare better on your next try." -- UChicago
"We rated your application as a self-professed theorist rather severely. We have few theory positions with support this year, and we had to therefore raise our cut. I don't think you could have done anything different to improve your chances except publish more, do more research, etc. all of which is somewhat unrealistic for an undergraduate in theory." -- Stony Brook U
"the real issue is not the weakness of your application but the exceptionally high ratio of the number of very good applicants to the number of places (alas, this is much worse for people from outside the UK/EU). For illustration - we were not able to offer a place to candidates who had offers from Princeton, Caltech and other top places." -- Oxford U