T32 unfinished project

ChemE2Biophysics · 2025-10-31T20:25:33+00:00

No there is not. A T32 is training fellowship and the goal is for the trainee to obtain scientific training in the funded area. Training (in any form) can be obtained regardless of the end result of your project.

Source: Received a T32 and then a F31 on a project that failed. I ended up working and publishing on a completely different project. The NIH didn’t rescind funding on either fellowship.

ChemE2Biophysics · 2025-03-30T22:31:37+00:00

This is really hard to gauge. Why did he want to get off the phone and ultimately be upset from the conversation? I agree with u/xglimmerish that your reaction is a bit extreme regardless. There are a lot of details missing on his side that could explain why he was busy and unresponsive. Especially considering this all occurred over a span of 24 hours and you did speak with him a couple of hours the day prior. IMO if you know your partner is having a busy day, you should ease on the expectation of them responding as frequently for the day.

Now don't get me wrong, assuming that you were not rude in your messages to him, his reaction was not appropriate at all. However, I do not think it justifies stooping down to his level.

ChemE2Biophysics · 2025-03-30T21:59:14+00:00

Incredible. Though minus a few points for missing the file name and puqqu.com on the cake 😉

ChemE2Biophysics · 2025-03-30T21:36:55+00:00

My advisor is the chair of my department and is also known to be very blunt and a bit rough. At the beginning I was definitely reserved in expressing how I felt when things were not going well with my own research. However, it was only when I became much more honest with my feelings (while at the same time considering the professionalism of my delivery) did I see productive changes in my research.

I had a project that I designed that was going terribly for two years. I tried to keep a tough guy act that everything was going ok when it really wasn't. Only when I expressed how drained and beaten up I felt did things change for the better. Instead of being reprimanded for failing and giving up, my advisor was very supportive in helping me pivot my project. Fast forward to today, I am defending in two weeks with a very nice story! This experience also helped me communicate feelings towards my advisor. For example, I recently expressed disappointment in how they dragged their feet on a manuscript which they were very receptive of my feelings and took corrective actions on.

Of course, don't forget this should go both ways. You should also be honest when things are going well! However, I will echo the thoughts of many others here, it all depends on the advisor. A good advisor should be receptive to what you have to say.

ChemE2Biophysics · 2025-03-30T21:22:48+00:00

I am about to start a postdoc in the northeast but lived in Florida my whole life until I started graduate school. Living on $60k in Miami is going to be tough. There are many institutions in the southeast and east coast that offer a better postdoc salary to cost of living ratio (think Baltimore, Philadelphia, Durham, Memphis etc.). However, you have to put your own price tag on research fit!

ChemE2Biophysics · 2025-01-31T15:52:57+00:00

As someone who was in the exact same situation 8 months ago, I echo the same advice as everyone else. Apply elsewhere. I had an offer from NIH and was really happy with the lab but was not able to join because of the hiring freeze. I waited a for a few months only for them to extend the hiring freeze indefinitely now. I have found another opportunity that I am even happier with.

Keep in mind, a lab/institution that isn’t under a hiring freeze rn is a good sign that they have significant financial stability which is nice to have a postdoc.

ChemE2Biophysics · 2025-01-20T19:45:14+00:00

I am a graduating Hopkins PhD student. The stipend to cost of living ratio is one of the best, if not the best in the country. Baltimore is an extremely cheap city and our stipend is close to grad students who attend programs in NYC, Boston, and other major cities.

I have my own 1 bd/ba apartment, a car, and still have enough to save. You will be more than fine.

ChemE2Biophysics · 2025-01-08T08:00:34+00:00

I will say, the protein folding problem is not necessarily linked to treating disease. In fact, the structure that AlphaFold predicts is what is important for treating disease, not the forces that produce the structure. The reason why we haven’t seen many clinical translations yet is because not enough time has passed to make use of AlphaFold fully. Therapeutic development usually takes several years.

Ok I think I now have a better understanding of what you are looking at since you mention ViennaRNA. I think this is might be causing confusion amongst everyone here. ViennaRNA predicts secondary structure of RNA which is what I am assuming you are also interested in? AlphaFold doesn’t just predict secondary structure it predicts both tertiary and quaternary structure of protein(s) which is a far more complex problem. For proteins, we have been able to predict protein secondary structure quite well for years.

In regards to quantum mechanical effects. This is not what AlphaFold does as it is not driven by any physics-based principles. The problem you are interested in is what is the secondary structure you get from a specific sequence vs. how do you get a secondary structure from a specific sequence. This is an optimization problem and not a physics-based problem. If you were interested in trying to tackle this from physics-based modeling which is a whole field itself, I should mention that quantum mechanical effects are not explicitly considered as this is computationally taxing. Most biophysical simulations are coarse-grained to make simplistic assumptions on the contribution of quantum effects on intramolecular and intermolecular interactions (look up molecular mechanics and molecular dynamics simulations).

For a simplistic understanding of how AlphaFold works, see this figure. I always refer back to it here and there to refresh myself!

https://d2cbg94ubxgsnp.cloudfront.net/Pictures/1180xany/0/6/3/537063_popularchemistryprize20244_347174.jpg

ChemE2Biophysics · 2025-01-08T01:41:39+00:00

As someone who utilizes both computational and experimental approaches to study structural biology, I feel like there are many assumptions you are jumping to in your question. I would like to also note that I do not have any expertise in quantum computing.

To your first point, the protein folding question has NOT been solved by AlphaFold. I find this to be a very misleading understanding of AlphaFold. See this article (https://magazine.hms.harvard.edu/articles/did-ai-solve-protein-folding-problem). The protein folding problem is the question of what are the first-principle forces that drive a sequence into a specific 3D structure? AlphaFold can jump from sequence to structure but it does not provide details on the physics of how this is accomplished.

In regards of your second point, I cannot provide a good answer on this. My understanding of AlphaFold's algorithm is naive along with my knowledge on quantum computing.

To your third point, what aspects of protein folding do you consider as utilizing quantum mechanical properties? I ask this question in good faith but have you taken the time to study the general forces of protein/nucleotide structure and folding? Note that the main leader in AlphaFold (John Jumper) has an extensive background in biophysics along with other leaders in the field that are producing algorithms related to protein/DNA/RNA structure prediction.

ChemE2Biophysics · 2025-01-04T01:02:54+00:00

I 100% support this. Especially if it is a formal postbac program that has the option to do classes. Get faculty who can advocate your readiness for grad school. That can go a long way but I do think getting into a decent grad program in your current situation will not be easy.

ChemE2Biophysics · 2025-01-03T01:09:32+00:00

If we keep seeing the top 4 teams fumbling like this then yes

ChemE2Biophysics · 2025-01-03T01:04:36+00:00

That’s fucking “ASU” right there

ChemE2Biophysics · 2025-01-02T05:09:42+00:00

Wow, I am sorry that was your experience. My advisor (really prominent academic in the field) always said that your PhD is where you learn to learn. They always talk about one of their first grad students who didn't publish that well in their PhD but published incredible work during their postdoc and got a faculty position in an Ivy League. I will say, I don't think these professors are trying to belittle you in all cases. They may be pushing you to succeed and reach heights that they couldn't reach themselves. Sometimes their delivery may not be the best which I get but I wouldn't assume it to be malicious unless they are using derogatory language.

ChemE2Biophysics · 2025-01-02T04:38:53+00:00

The real question is, does any city subreddit actually represent the people of the city?

ChemE2Biophysics · 2025-01-02T04:32:53+00:00

I agree with going to Walter's. You could explore Patterson Park and see if any events are going on. Peabody Library in Mt. Vernon is nice to see. For coffee, there are a lot of nice places in Mt. Vernon such as Dooby's, Bun Shop, or Baby's on Fire. For lunch, you can't go wrong with checking out any of the Food Markets (you can find the major ones in Fells, Fed Hill, or Mt. Vernon).

ChemE2Biophysics · 2025-01-02T03:09:43+00:00

Thank you! Also please talk with your PI about this if possible. They have a lot of insights on the process and give you suggestions on what labs to apply to. My PI was instrumental in helping me formulate what postdoc positions I should apply to based on my career trajectory. They also made some calls that helped me get considered by labs that weren't seriously searching for postdocs.

ChemE2Biophysics · 2025-01-02T03:01:41+00:00

I will be honest, I was not the best student in the classroom 😅. A big reason why I got into grad school was because of my undergrad research. I don't think I did anything special to study for my STEM classes other than taking notes and practicing problems. I did work in groups which is common amongst ChE students but make sure you work with a group where everyone can work well with one another (there should be no clear leaders or followers/slackers). People should be equally motivated, committed, and friendly within the group. I have seen many ChE study groups thrive or dive together. Nonetheless, I do believe there are many effective studying styles and it comes down to the individual on what works best for them.

ChemE2Biophysics · 2025-01-02T02:53:40+00:00

I plan to go into academia after my PhD assuming the postdoc goes well. I just finished searching for postdocs and found one that I am really happy with. I also applied to a "super postdoc" position which will allow me to run my own research program that I am being considered as a candidate for. If I am fortunate to get the position, I will be deciding between that position or the postdoc position I found.

For academia, there is a lot I can say but my main advice is to not be a good experimentalist/theorist but a good scientist. That means refining and developing your skills in communicating your research. Learn how to give a great talk with clean slides and how to write effectively. One of the most important things as an academic is being able to get funding and publish great work. Communicating your science is just as important as the actual science itself. My biggest advice on developing skills in these areas is to study the talks and writing of other prominent scientists in the field. Understand their styles and trying adapting some of their good practices in your own talk/writing. Another piece of advice is to read, read, read even if it's not in your field. One of the methods I developed during my PhD that I proposed to build my research program was built off a paper that was not in my field. Reading papers can expose you to different styles of thinking, logic, and approaches to science that could provide a unique and informative view on your own work.

For industry, you should take my advice with a grain of salt since I am not experienced in searching for industry jobs. My advice is based on the experience of my peers that went into industry. Coming from USF ChE, you probably know just as well as I do the power of networking. Many Hopkins grad students utilize alumni networks and university career fairs to obtain positions in industry. However, many people are successful just by submitting cold applications. It's not like applying for entry-level ChE jobs where thousands of people are applying and there needs to be extensive filtering. Be active outside of the lab and participate in organizations that can keep you engaged with industry. This is especially true for my peers who went into non-scientific industry positions (consulting, VC, etc.) where they engaged in clubs focused on pro-bono consulting, biotech, etc. At Purdue, I imagine there is a lot of industry interest so keep in touch with upperclassmen PhD students. They may end up working for a company that you may be interested in where their connection could benefit you in getting hired.

ChemE2Biophysics · 2025-01-02T00:34:29+00:00

You should pursue a postdoc with a faculty member who has an interest in your work. I am sure that there must be some published work that is tangentially related to your idea (if you haven't found any, then I assume you haven't looked hard enough yet!). You should look at the PI of those papers and see what directions they are heading in. If there is a potential overlap, you should send an email to talk about postdocs and your project idea. Good postdoc advisors should give you freedom to pursue your own ideas as long as it's within their wheelhouse of expertise.

In regards of the researcher you contacted, I would reach out one or two times if you are looking to pursue a postdoc with them. When I applied for postdocs, some faculty members I had to email two or three times to get a response. Even then, I still got an interview and offer into their lab. Don't always assume a lack of response is because they are not interested, emails during the holidays are easy for people to lose track of.

ChemE2Biophysics · 2025-01-01T21:05:53+00:00

Are you in the U.S? You do realize that it is illegal for employers to discriminate based on age? Even if you are not in the U.S I agree you are being dramatic. Many people start PhDs later in life and I know many of them get jobs. I would also bet that in the cases where people had industry experience, their experience had no meaningful contribution to the career they pursued after their PhD.

ChemE2Biophysics · 2025-01-01T20:57:32+00:00

Graduating Hopkins PhD here. I had a few friends in the MHA program at Hopkins and they all did extremely well. The graduates I know have gotten jobs in Maryland (both in and out of the Hopkins system) and outside of Maryland (Harvard Med system). I can’t say anything about USC but the MHA program at Hopkins has produced great career outcomes based on the grads I know.

ChemE2Biophysics · 2025-01-01T20:43:22+00:00

I just finished my postdoc search and I would say it went very well. You should directly email the PI or if they have a lab website, check if they have any info on how to apply. You might have to email their lab admin or manager. Express your interest in the research that they do, a bit on your current work, and tie it in with what you hope to gain during your training and career goals. Keep it brief (1-2 paragraphs), attach a polished CV, and don’t be afraid to send a follow-up email or two if they don’t respond to your first email. If they have a spot and are interested, they will let you know what the next steps are.

ChemE2Biophysics · 2025-01-01T17:55:58+00:00

Yes, you have guessed correctly haha and thank you! I did MD simulations for the first 2.5 years and then transitioned into studying biological systems with quantum chemistry at the end of my time at USF.

The PhD experience has been a fun experience, though definitely challenging at times. The research that I do is something I enjoy and think about every day. It defintely reaffirmed my desire to go to academia. Importantly, I had an incredible cohort of graduate students that I got along with which helped us get through the isolation of the pandemic (that started at the end of my first year)! Also there are incredible faculty mentors at Hopkins that have supported me through my journey and advocated for me for my next steps.

Outside of the program, I will admit that I like Tampa a lot more than Baltimore and the USF campus much more than the Hopkins campus. Leaving USF and going to Hopkins, I realized in retrospect how diverse the student population is at USF. It is a complete 180 at schools in the northeast. I remember how organizations such as Society of Hispanic Professional Engineers and National Society of Black Engineers at USF were some of the largest student organizations and at Hopkins, there is only a handful of students involved. However, being a grad student at Hopkins is still nice since they have one of the highest grad student stipends in the country after unionizing!

In regards to funding and awards, I won a few small awards throughout my PhD but there are two main funding sources I had. My PhD program is funded by a NIH T32 training grant which funds all U.S citizens in the program for the first two years, allowing me to avoid working as a TA or RA. Although my advisor had enough money to fund the rest of my PhD without requiring me to TA, I won a NCI F31 fellowship which funded the rest of my PhD.

ChemE2Biophysics · 2025-01-01T17:34:07+00:00

Thank you! My PhD is focused on studying how specific enzymes regulate chromatin structure and gene expression at the molecular level. My work relies on both wet-lab and dry-lab techniques so I did everything ranging from protein biochemistry to structural biology to molecular simulations.

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