TakeruK wrote:It's pretty hard to tell, since there are a lot of unknowns still. I would guess that whatever schools accepted you the first time around (i.e. Fall 2012?) might accept you again for Fall 2014 after you finish your Masters, especially if your profs write you strong letters! I'm not sure if the schools that rejected you in the last round would change their mind this time, since it does not sound like your profile would have changed very much since the last round. Sure, you would have completed the core courses (although at time of application, not all of them might be complete) but the classical/statistical mechanics failures would be a big flag (especially since many undergrads applying directly to PhD schools would have already passed their undergrad stat mech class at a high level).
As for staying at the same school, only your program can answer that. I'd imagine there is some departmental policy on the requirements to continue in a PhD program, so you have to talk to your profs and figure out what you can do to meet those requirements. If they allow you to stay, then, in my opinion, this might be the best way to finish your PhD, but you should definitely apply to other schools for Fall 2014 as well, to keep options open.
Thanks for your reply TakeruK.
From what my profs told me, my guess is that I should be getting strong letters, in spite of what has happened. I have sort of short-listed some schools, but most of them are places where I'll be applying for the first time and so, I don't have much idea as what to expect. At the time of application, I will be done with 4/6 of the core courses. I intend to improve my GPA in the coming semester, which hopefully should help in the admission process. Classical failure will be covered soon by retaking its qual before application process, and so my guess is that it shouldn't be a problem, since I come from engineering background without having taken any physics courses! I do agree that its a shame I did bad in that course, but as I said before, I was seeing that material for first time. Anyway, as with applications, I have no idea what kind of schools would be ready to accept me, as I'm applying to whole different schools than in 2012.
And about staying at my present school, I have talked to some senior grad students and they advised me to just pass the quals and make an appeal to the department to consider me for PhD program. But, for now, I do have to be prepared for the application process!