biochemistry professor

Yes, much more difficult for intl students because of lack of recognition of international schools outside of top 20 schools such as Oxford, Cambridge, etc. We also get many students from developing countries who turn out to be complete busts because of the poor preparation they received in their home country or failure to adjust to cultural differences.

Looks great. You should be competitive (not a shoo-in) anywhere!

You have a chance (but perhaps not a good one) at the top schools, but you need to also apply to some less competitive programs to make sure you get in somewhere.

You need to retake and do much better on the TOEFL. Otherwise, there's not much professors can do for you. If you do well on the TOEFL, you'll be a very attractive candidate!

Why are you failing your classes? How will you improve your academic performance so you can do well in the much more difficult graduate classes?

Rankings can be useful, but you need to take them with a big grain of salt. Apply a +/-15 to them. Schools love to talk about how useless rankings are but brag that they are ranked highly. One of the most important reasons why schools care about rankings is that the rankings help attract students. At a higher ranked program, your peers will generally be stronger. You will learn more from them, and they will form the core of your future professional network. Prestige and reputation can be important if you move into a career outside your graduate training. Many graduates will not continue in chemistry or science. For example, if you move on to a career in patent law, it will be generally more helpful to have attended a big name school than a less recognized school with a strong program in subdiscipline X. If you intend to make your career in a certain location, it can be more beneficial to attend the state flagship than a higher ranked school far away.

Exceptions can usually be made for cases where an applicant barely misses a cutoff like TOEFL or GPA. However, our experience with students with weaker English ability is that they really struggle academically even if they have a strong science background. And they make terrible TAs. Please devote as much time to improving your language skills as your science.

You'd competing against other MS graduates with recent MS level research experience. The decision to pursue a computational degree may be interpreted as a choice to move away from experimental work.

I think your accomplishments and work ethic are great, but I want to share how grad programs think. It is better to have a research advisor attest to your work ethic. Focus on the science. Talk about your science accomplishments and how you are looking forward to focusing 100% of your time in grad school to research instead of part time jobs (which I hope is true).

At the most competitive places, I think your research record could raise some red flags. Doing research takes a lot of perseverance and the ability and patience to grind through a lot of rather repetitive work. You don't want to come across as a professional student. I'd downplay the range of your experience (especially doing a computational project with one professor while working in another lab!).

Not many computational jobs in science. The majority of science jobs require lab skills, and you will be heavily disadvantaged. However, computational skills open the door to a wider variety of non-science related jobs involving math and computers.

Don't send a non-science related LOR from your job. There are potential concerns with non-traditional students who worked a lot during college. One is whether you have serious family or financial obligations that will be an obstacle during grad school. Grad school stipends are small, and you will not be able to take a part-time job. Another concern is the rigor of your preparation since you were able to get a 4.0 while working so many hours.

Having real world experience and maturity is a big plus. There are too many students coming out of college who aren't serious enough about grad school and being a professional.

Sounds like a bad fit. Don't expect anything more than him. Cut your losses.

Never choose a MS program you have to pay for. There are schools with funded MS programs. It sounds like the PhD program is a good option for you. Work hard, develop your passion, and publish like crazy, and you will be fine.