Research Update: Post Quals

Since I’ve finished up my qualifying exams and adjusting to life as a PhD candidate where my sole graduate school responsibility is doing research, I figured it was time for an update on how those things are going!

I’ll start with the second project. Now that I have completed my second year, I no longer have the obligation to be working on two projects simultaneously. Some students take time after their exams to tie things up with their second projects while others continue doing work on the side long after they’ve passed their exams. For me – I had a nice compact little project that was pretty much finished when I reached the point to take my exams. So! No more allan variance and spectrometers for me! Some time I should compact that report into a nice blog post…

So now it’s all outflows all the time. Also in preparation for my exams, I wrote my first academic paper of my graduate career. [Fun fact; the paper I wrote with my undergraduate advisor finally (after two years of it sitting around and needing to be edited) got published in the past few months too!] Working on this paper took most of my attention after I finished my exams. To get an academic paper published there are seven-ish steps;

  1. Write the paper
  2. Check with your collaborators that they’re happy with it
  3. Submit! At this point the journal assigns a peer reviewer to your paper and you wait for their response
  4. Once you receive this referee report, you edit the paper accordingly. This involves both small grammatical edits as well as major science edits. As you work through this you put together a cover letter responding to your referee, either informing them of how you addressed the edit or responding with an explanation as to why you didn’t make the edit (though most edits are treated as mandatory)
  5. Resubmit!
  6. You may repeat steps 4 and 5 if need be…
  7. Once they’re happy with it you deal with all the logistics of it being published, like reviewing final manuscripts, paying publishing fees to the journal, etc.

I am currently at step 5. I made sure the first submission was in before April and that left me most of the time between then and my exams to study. I received the referee report shortly after my exams and spent the next few weeks working on the edits.

Overall I got pretty good feedback – the response stated that my work was worth publishing as long as I made some points more clear. However, in the meantime, my advisor and I had realized I could have done one of the applications in a more practical way – so a lot of my editing for the paper was re-doing some of the work I had done before.

By the beginning of June, the paper was resubmitted and I was back to research!

Now time for some science! So my first paper was on the majority of the work I did in my first two years of graduate school. I was analyzing simulations my advisor had previously run of galaxy outflows, and deriving observable properties – so I was taking a simulation and figuring out what an observer would see if they were to actually see it in space! This involved estimating what kinds of material would be in these outflows, which ions (a specific type of each atom; for example; carbon is an atom, but carbon IV is an ion – meaning that it is a carbon atom that has lost four electrons) are in the gas. I could then ‘measure’ the amount of each of these ions in the simulations and estimate what that would look like to an observational astronomer. To do this I had to make a lot of assumptions including the fact that whatever way these ions were created – or whatever was causing the atoms to lose electrons – was something I could estimate after the fact, or it was not something that needed to be accounted for as the simulation was running.

Turns out that this assumption could make a big difference between the results I get! So the next step is to run my own set of simulations that mirror the ones I was studying, except this time the chemistry aspect of the creation of ions will be accounted for within the simulations, in runtime. Getting this to work has been the main goal of my work for the past month. Okay, most science over… 

In order to run a new set of simulations to study – now with chemistry included; I’ve had to download and install the various packages that allow for the chemistry to be calculated, I’ve dealt with many other random bugs in the code, I’ve created the necessary reference files so my code runs how I want it to, I’ve needed to decipher the data into something that makes sense, and I’ve been doing tests to make sure the code is working as it’s supposed to. That’s where I am now – I’ve gotten everything working (it seems) but there’s something that appears fundamentally different in this chemistry run than the previous ones.

When I’ve figured out what to do about that current bug – I should be off to the races and running oodles of simulations to create the set of simulations I will then get to study. Exciting stuff.

As one final update – now that I have nothing better to do than work on research, I have a lot of flexibility in my schedule. This can be a bit annoying – in that it’s on me to maintain a normal work schedule – but it can also have some great benefits. I’m not obligated to be anywhere, I don’t have classes to attend or assignments to turn in. I could, say… travel to Germany… for say… 4 weeks… and actually, that’s what I get to do!!

I’ll be going to Germany for 4 weeks in mid October to work with a collaborator there. Since coming to grad school I have wanted to work on simulations involving magnetic fields. In order to do this, I need to learn a simulation code, and a collaborator of my advisor has just hired someone who works with this code regularly. So a research grant is paying to fly me to Germany to learn this new code. Pretty great. 🙂

4 thoughts on “Research Update: Post Quals

  1. Great update! When you say Oodles I’d simulations….. what’s a ballpark for “oodles”? 🙂

    I’m excited for you to get to go to Hamburg and work with this simulation code. And to just visit Germany. Yay Adventure!

  2. Fabulous J’neill. cudos for work well done 👍 I’m So happy for you 😊💓

  3. Congratulations! These simulations that you are running is all on the computer – ccorrect? I’m curious what, if anything, you imagine in your mind as you review them… like do you see space and stars and colorful nebula in your imagination, or it it more mathematical? Or ?

    I’m curious about this because of a conversation your mom and I had about our internal perceptions of time and how we see it in our minds (very different from each other)

  4. But what about real run-time simulations for what is causing the proximate chemistry resulting in carbon ions, and then also, simultaneously simulating what is causing the cause of the proximate ionic creation, infinitely regressing back from that, in the SAME run-time simulation, i.e. how has the universe(s) “really” been working? Just a mini challenge for you!

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