PhD application with mediocre grades, 2 SCI co-authored pubs., LORs from very well knows profs. in the area?

I am going to start my master thesis now. During my master I performed not well, my GPA is about 2.9/4 which is really bad for me. I am not excusing but my mother had cancer and she died in september, even though I studied very hard I performed poorly in my exams. I would like to apply a PhD program when I graduate, however I scare like a little rat due to my low GPA. On the other hand, I have two co-authored publications in not excellent but very good journals. Moreover, I have been working two of my professors about 1 year and going to start my master thesis with them which would be really good I think. Furthermore, my university and department is well respected in the Europe.

Actually my main fear is that, in my transcript my low graded courses are in very tangent to my thesis and past projects that I made with those two profs. I believe that in the future, when the evaluator look at my application folder he would be very suprised about my transcript and qualifications, the discrepancy. When I said my grades during this semester to my advisors, they are shocked as I expected. I fear that, that discrepancy would form second thoughts in people's mind.

So my question is, as far as I cannot change my GPA anymore. What should I do more to contribute my application, and show to people actually I know the subject in contrast to my low grades?

This is not a duplicate question, I am asking what should I do. I am not asking the admission process, furthermore I am not in border imo.