Research Updates | November 2020

November Calendar (October/December)
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This is an ongoing post of research updates during the month. Updates are provided every few days, and you can easily reach the update by clicking the link in the calendar.
11/4/20 – Plans for the month and election update

I have quite a few things to accomplish for the month. Lets break it down.

  1. With my first draft finished, I need to move forward with the Pluto results. I think, I would like to have this mapped by our next meeting (11/18/20) and have the depth profiles by the end of the month (12/2/20). Then we can set up a meeting with collaborator in December to decide how to move forward.
  2. Catherine and I have a meeting 11/13/20 with McGill. I need to prepare for that. That will include reviewing notes from last time and prepare for updates from the team. What I hope to bring is 1) my own results and plans to move forward and 2) a proposal for an experiment idea we discussed before. That is, an experimental apparatus to model an organic freezing in water to test the SF2 model.
  3. On that note, I need to think about how to move forward. That means adapt the SF2 model to work with an alternative chemistry, ideally an amino acid that is denser than water. The first steps mean reviewing the material we have on how it acts in water like with HCN. At the same time, I would like to update my results for my paper while it is being edited by me and my coauthors. I have the SF2 results; I need to process them to get a new set of fits (extrapolation) and thermal model. I think I can do this in the amount of time edits will take. However, I would like feedback on if this is necessary. If yes, lets aim for final results by end of the month. Similarly, I would like to have my initial research for an alternative chemistry by the end of the month. That paves the way for implementation in December.
  4. In the same vain, I need to put together a presentation for my lab on some topics discussed in my PhD comps. This is related to chemistry and the water-organic relationship, so I think the two goals go hand in hand. The goal is to present these results in December.
  5. Lastly, I need to make a poster of my results. I think I will just apply my presentation. I am not sure what the timeline is for AGU, and I’ll decide on this later in the month.

In other news, one of the worst scenarios is playing out in the election. That is, Biden’s path to victory is a slow one dependent on absentee ballots. Trump has already screamed fraud and called for them not to be counted. If this isn’t a crime I don’t know what is.

An image of the already marked tweet made by Trump. Note, the first version of this tweet misspelled the word “polls” as “poles”.
11/18/20 grading and editing and last minute modeling

Earlier this month we had the Dragonfly meeting. That was a long yet fascinating experience. I look forward to following future meetings. I’m in a bit of a unique position to join titan research at the end of a long mission (Cassini), and now I get to watch the making of one. It was at times a little technical for me, but I still enjoyed the experience. Naturally, I wish it had been in person. Not only for the lovely trip to Baltimore (or wherever it would have been), but because it’s difficult to stay focused behind a screen with no one around to see you distracted.

I’ve also been working on the second draft of my HCN paper. Catherine had some great advice (naturally) on how to improve the paper and the results which involved a few more model runs. Luckily, I had already been running more models since I was finalizing the paper, so I was in a position to update my results right away. Unfortunately, things did not go as planned.

When I was finalizing my first draft, I tabulated my variables and constants in my model. Naturally, I validated all the sources I had listed for my values in my code. It was then that I noticed I had one of my values off or my source had changed. I updated it, but it didn’t seem like a major update so I didn’t expect it to change much. However, after looking at the new data I had ran while I edited my first draft, I realized it was a fairly significant offset. Que full system check.

I did several things. One, I reran all my codes for new results. What I found was that updating my values had streamlined the code. It ran faster, and worked at more extremes that it struggled with before. This means, if correct, I may not have to extrapolate. Then second, I needed to make sure the change was because I updated my values and not a major mistake in the code I made. This meant I tried to recreate my old code with the old results. As hard as I tried, I couldn’t do it. I wouldn’t say I tried everything, but I felt like I could only afford so much time for this. Alternatively, I downloaded Jacobs fresh code and input the values as my current sources documented them. It reproduced my most recent results. This means, while I may not be able to recreate my original results (which concerns me), I can at least test assured that the change isn’t a mistake I made in the main code in some other area. All I can say is, my parameter values are accurate, and I can reproduce these results from scratch.

Example results with original data and new data. New data is on the right, with the added overlap at the top right starting from scratch with Jacob’s code. Notice the artifact on the left red line that no longer exists. This is comforting because it did not make sense, and was a big reason why I couldn’t use higher concentrations because it seemingly wasn’t stable enough.

I have some ideas on what was the key change that caused the results to change. However, without investing more time on troubleshooting I chat say for sure. One thing I have failed to do, largely because of confusion, is install GitHub which I believe saves various versions of your code for reference. This would have made troubleshooting a much easier process.

For now, I have been reproducing all my results, and more. To the point that, I think I won’t need to use extrapolation. However, I am pushing my luck when it comes to finalizing this second draft by Friday. I very well may be able to finalize my SF2 model results today and begin the heat transfer model. Although, I have doubts. It seems very likely this is going to take a few more days. If I don’t get this buy Friday (I have lab Thursday too), I think next Wednesday is achievable.

Fall Meeting 2020: Scientific program now online - AGU Newsroom
The yearly AGU conference is online where I will be presenting a poster.

I have not even mentioned that my AGU poster is due Friday. That will be done today, perhaps tomorrow, so I have time for feedback from Catherine.

PS: my power was out when I woke up this morning which meant I one, woke up late despite planning to write this, and two, had to write this in my phone.

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