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I'm currently pursuing an M.Sc. in Europe. I am going to apply for a PhD program at an Ivy league university. I am afraid that some bad marks in the master's (especially one in a relevant subject) would affect my application.

Some background: I completed my B.Sc. in mathematics with very good marks (corresponding to a GPA of 4.0 or something close to it) in Europe and then moved to another country (still in Europe) to do a quite renowned master in theoretical physics (about 1 out of every 5 applicants was selected for this master).

Current situation: Because of several factors (moving to another country, changing subject from math to theoretical physics, different and stricter exam regulations*, having chosen to follow the most demanding courses) I got bad marks in my first semester. In particular I got the American equivalent to 2.5 in a subject which is relevant for my master thesis (and for the PhD project I would like to pursue). During the second semester my grades improved. Since I got most of the required credits, I have time to do the specific low-grade exam again during next semester (I can also do more exams to replace the bad ones according to the university regulations).

Problem: Even if I do the exam again and get a good mark, I will know the results after the deadline of the application for the PhD. So, I can't reflect my ability in that core subject (apart from my results in other exams and from my reference letters) in the application. Would it be a problem for my application? Would saying "I did bad in the first semester but I will try to make up for it in the third semester" be satisfying for such elite universities? I am very excited about the research topic and would love to work on it. I am just afraid that some bad marks could affect my chances to get in the PhD program.

Additional info: The PhD program would be in physics / theoretical physics. My B.Sc. was in mathematics but included physics exams (and I did more physics exams than average by choosing optional modules).

*here I mean that in the master's I had less time to prepare for exams (they were immediately after the end of the lectures, whereas during my bachelor's I had time between the end of lectures and the exam session). Moreover, in the bachelor's I had multiple retake exams and every retake had the same difficulty whereas here we have at most one retake and if it occurs it is more difficult than the first exam (this is an objective observation claimed by professors, I quote "you can't get a good mark at the retake" and "guys I suggest you to do the exam immediately because the retake will be way more difficult").

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    I've occasionally had the same experience with apparently random downvotes. I didn't see an issue with your question so I upvoted it back. – G. Allen Aug 24 '20 at 13:51
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    Mistakes happen. If you feel that you know what exactly went wrong and how you can improve on it, explain your plan for improving any weaknesses in your statement of purpose. – Daveguy Aug 24 '20 at 21:17
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    Since you are saying Ivy league I take it you are applying in the US? in which case did you sit a GRE physics for the application? If that is high enough then maybe you can compare using that (though I don't know inner details on how the US application system works). The other thing about the US is that the PhD program includes the master component for the first couple of years, so in a sense you are going to be doing masters courses. – N A McMahon Aug 27 '20 at 15:44
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    Why applying at an Ivy League uni? if your goal is to get a good PhD, apply to the EU Marie Curie scolarship and then you will have the freedom to bring money to any lab/institution, your CV will look so much better (proving you are able to get funds independently for your research, a skill much required and sought after on both side of the Atlantic Ocean). I do not say Ivy league are bad choices. I am saying there are better choices, which in the long term will quickstart your path to a professorship, with less risk of being involved in accidents in a racist, violent, inequal country. – EarlGrey Aug 28 '20 at 7:17
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    @moonlight I have a strong opinion on that, but during your PhD you will get at best 10 hours of your professor time. It is not particularly relevant to have them around you. It is much more efficent that you are doing your PhD "somewhere" and you prove you are capable in the specific field X, so during your PhD you can be a visiting at professor of field X for 3/6 months. I have a strong opinion, my experience is that during your PhD you need to learn t ofly on your own, then you can join the storm of the top 1%. Being with them to learn to fly it is usually bringing people to burnout – EarlGrey Aug 28 '20 at 8:42
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I believe it is very normal to have some drawbacks in every university experience, especially in the situation you described. I believe most people would be understanding if you explained to them what caused that specific grade (the changing masters and countries, etc), and I would explain how you are improving (extra hours of study, asking for advise of older students, learning better organization techniques, things of that kind). It's all a matter of how you expose the situation; if you expose it with a positive output, they will get a positive impression of you!

For my master thesis internship interview, one of the topics I talked about was how I in one semester had very low grades (average of 13/20) and even failed at one subject, and how I decided to turn things back around, got up on my feet and in the next semester, did one extra subject and ended with an average of 18/20, and they loved it, I was actually their first option for the internship! It's all about how you deliver the info :)

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I can relate to your situation, as Johanna stated above, it is normal to feel like you might not be on par with other applicants. As far as lower than desired GPA, or any other factor that you may be holding you back, one of the things that the Ivy Leagues (and other schools in the US for that matter) generally require for PhD admissions is a statement of purpose, where you explain why you are applying to the programs you are applying to as well as your research interests. It's been discussed in a couple other posts on this site, but the statement of purpose (SOP) is a great place to explain any hiccups that may have occurred during your previous education (people tend to be more understanding of stumbles along the way than you may think). So in the case of your low grades, you could briefly mention your low grades, and what caused this and how you improved from that situation and how you plan to build on this during your PhD studies. You want to remember, though, to not bring too much (negative) attention to this and keep everything in a positive light here.

You are far from the only one I've seen on here to post worrying about lower than desired grades; a lot of people have posted fretting not being able to get into a PhD/graduate program due to lower than desired grades, most often owing to a bad first semester or even first couple of years. However, a lot of people have overcome such situations and have been able to secure admission to great graduate programs, so keep your chin up and eventually things will work out. Hope this helped and best of luck.

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This is exactly the sort of situation that a reference letter should address. Find a referee, perhaps the lecturer for that subject, who can credibly say that your results don't truly reflect your ability and explain why.

(Of course, as other posters have suggested, you can also explain the situation in your own statement. But this might look a bit defensive, which is why it's so helpful to have someone else, who can take a more objective tone, do it for you.)

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How were your GRE scores? If they were great, you can write off that one bad grade, maybe even show semester-by-semester Marks to prove it’s an outlier. If your GRE scores were poor, there’s a chance it will be seen as confirmatory that your poor grade was diagnostic.

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