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.
2/4/20 – Leveling off after a bumpy start
Monday wasn’t the best day. I didn’t reach my timer goals, but I managed to make them up today while still managing six today as well. It makes me feel a bit better about the week. That said, I look at the progress I’ve made on these labs and it terrifies me. I spent all of today grading, even though I know I shouldn’t. Tomorrow I’m going to refocus on background review for comps. Jahnavi and I are trying to work together, each studying a different topic and coming together to discuss each with one another. The goal is to hold ourselves accountable while lightening the load a bit. That is, we each help in finding good sources for different topics.
I went ahead and started a few models to expand on the data I have. I am facing a serious problem with models in the 100s of ppt. I can’t figure out why the model doesn’t want to work, and I’m afraid it may take me spending a good amount of time troubleshooting it. There is also a problem with the data where it spikes at a certain depth for all my concentrations. I need to figure out why. Imagine the curve following a set path, then you take a slice and slide it to the right. That is basically what is happening at maybe 50 m depth for each depth.
Wednesday was a good day, spent grading, but productive nonetheless. I managed 6 pomodoro’s even after the lab meeting. Those labs are almost done. Although, now I have a new set. I think I am going to have to start logging exactly how much time I am working and even do grading on my own time. Honestly, I don’t mind tedious labs because I can listen to audiobooks while I go through numbers and one word answers, but short responses require I actually think about what they’re saying.
This weeks lab was on “Is it Science,” which is always fun. Of course, I would always refer the reader to Carl Sagan’s The Demon Haunted World: Science as a Candle in the Dark among other works by him. This also marks my last lab until lab 10, so that will help me moving forward (especially with LPSC around the corner).
2/11/20 – Grading and Deceptacon (Visiting Atlanta)
I’m leaving to go to Atlanta tomorrow night for Deceptacon. It isn’t the best timing because I have so much grading to do on top of my proposal being due soon. I’ve been focusing mostly on the grading to get it out of the way. I’m also hoping to make time to get some grading done while I am away. Reading week will give me some time to get ahead in my grading.
Sadly, this was not a productive trip home in any way. I didn’t get any grading done, and I never spent much time focused on my proposal. On top of all that, I fell behind on my Youtube and reading schedule too. You’d think a time away from work would mean I have more free time to do the things I like. Sadly, I just couldn’t get in the mindset to do it. It isn’t all bad, though. I had a lot of fun playing werewolf and seeing my friends. I actually got more sleep than normal too getting to be at ~10 PM the first night and ~12 AM the second night. Admittedly, I literally didn’t sleep the last night, but I knew I probably wouldn’t. That’s why I didn’t feel as bad missing time to play the first two nights to ensure I had a couple full nights rests. Now that I am back I have to refocus onto labs and proposal.
Everything is coming down to the wire. The astrobiology midterm is barely a week away, yet I am still behind on my labs. My proposal is due in like three days. You would think that these two deadlines would motivate me, but that just wasn’t the case. This all has me very anxious and stressed about all I have to do, and instead of working, I am doing less work than I normally do. Honestly, this has probably been the worst productive week this year.
Even outside of school, when I am at home I can’t help but stress about my lack of work at school and thus feel like I can’t stop and read. Of course, I don’t work, instead I just sit down and watch TV, and the result is that I end up reading next to nothing. That sucks because I like reading. It’s relaxing, educational, but it has also become a fantastic way of structuring my work-life balance. I’ll be relieved when this month is over. For now, it looks like I’ll be having a weekend of working from home.
It took a lot of time, but I finished the proposal. I didn’t even have to postpone the deadline. I also finished one of the labs I have been grading which gives me time before I do the next one. I ended up tackling my proposal by asking which parts I had left. Then I made an item in my pomodoro timer for each section asking how much time each section ought to take. Then it shows me 1) how much I’ve done and 2) how much I have left. It really helped me focus, but it also kept me from focusing too much on minor sections that weren’t worth that much time.
In the end, I did ~30 pomodoros. With a daily goal of ~6-8, that equates to roughly 5 days of work. That doesn’t even include the time I spent grading. Obviously, this doesn’t change the fact that I have more to do. I still have to create updated drafts for the proposal and keep grading, but it is still a relief to be able to say I did what I needed to up to this point. It’s also nice to be able to look back on the work I did and quantify it. Sure, I had a bad week last week, but this pretty much makes up for it. That alone is helpful in breaking free of this spiral of stress and self destruction.
This week, I will finish another lab and hopefully get a final draft of the proposal finished too. Outside of school, I am working to make a final sprint of reading to make up, at least in part, for the sluggish couple weeks I experienced. I am hopeful moving forward that I will make good progress all around!
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.
1/6/20 – A new month, year, and decade
I had one hell of a trip back on Saturday. I had just come down with the flu which made my trek home a miserable one. Add on to that the two hour late Greyhound I had from Detroit (to London) I was about ready to die. Nevertheless, I made it home. Friday I submitted my revisions, and I was able to submit it under the Cassini submission (yay!). Today I got the edits back from my collaborator for my LPSC abstract. I still have the flu, so I am not that eager to finish it just yet.
The flu didn’t go away until Thursday. That was a blessing since it was also the first day of lab. I finished my LPSC abstract in a flu induced daze. Most of my week was spent at home in bed resting. The first astrobiology lab went fine. The set up was annoying, as was coordinating with the professor to ensure we had all the proper items for the lab (apples, sugar, etc.).
Given the flu, I didn’t do much time management techniques. I did some work reproducing my model. I spent much of December reviewing it and the models it is based on, but I am at the point where I have to start applying it. My goal for next week is to focus on that as well as get back into the Pomodoro timer, which Catherine has suggested a much more reasonable goal which I am excited about (the reasonableness of it that is).
I’ve had a more successful couple days of 6-8 pomodoro’s. Part of me feels I ought to be doing more, but it definitely is a much more attainable goal. I’ve also found myself keeping a much more regular sleep schedule which has helped form a more structured routine. Hopefully it sticks.
I spent some time doing TA duties for Astrobiology. It is a little frustrating because Jahnavi and I have yet to get an official duties sheet from the professor. That means it is a little unclear what our responsibilities are. Obviously, I’ve done the class before, but is he expecting us to handle the course project. He’s having us receive the relevant information which suggests we are handling it, but a bit more guidance would be appreciated.
As for the model, I’ve been able to piece together how a few components are implemented. That is, it makes sense, and I can replicate it, but there is one piece that is very convoluted. It is unclear how it is making use of the governing equations. I have an idea of how I would apply them, but it isn’t what I am seeing in the code. I’m discussing this with Jacob to understand what it is he’s done, but I am also going to review a bit of finite element modeling to make sure I’m up to date with the material.
I still haven’t replicated the code, but after a bit of thought plus a little help from Jacob (code maker) I was able to figure out what was going on. It’s a straightforward application of the equations that set the gravity driven brine velocity, the ice fraction, and the Raleigh number used in the model. I was confused when it came to solving for temperature and salinity.
The actual solution is a bit more complicated as it uses a method in linear algebra to expedite the solution. Again, I couldn’t replicate this (as it stands), but I think that is okay?
This wasn’t a great week. In addition to having lab on Thursday to do and prepare for, I had grading for the previous weeks lab. That was exacerbated by having to sub-lecture for Nigel, the professor of the course, on Tuesday. It was one of those weeks where I get overwhelmed and become less productive and feel worse. I didn’t do any pamadora timers, and I think that was part of the problem. Luckily Nigel got back from his conference early and was able to lecture on Thursday, and that was a bigger relief than I realized. I was able to focus on grading the rest of the day and Friday (for a bit).
In terms of research, I did a bit of work trying to check the progress of the models I’ve been running the last few weeks as I review how it works. Obviously, it hasn’t been a major priority, but I didn’t want that time to go to waste. I am at a bit of an obstacle because I can’t get it to work for over 200 ppt (20%). I’ve been troubleshooting that because I want more data to present for LPSC in a couple months.
I’ve had a hard start to the week as I’m not using the timer. I have a lot of grading and other astrobiology work, and I am worried I am spending too much time on that. It is just very easy to gravitate toward that, and it ends up taking up a lot of my time. I need to just restrict myself to a set number of timers a day for that because what I am doing right now is just not even bothering with the timer when working on astrobiology stuff.
I spent some time reviewing my work on the model, less review and more checking on my state of results. There isn’t much progress to show in this regard as of yet. Overall, the end of January has been very sluggish, and I am going to aim for a more productive February. I can use Pomodoro’s every day, save Thursday’s. That is my goal; use these every day with a clear outline of what I did and on what. If it’s a slow day, then it’s a long day.
Much to my surprise, I received a presentation at LPSC. That is equally exciting and terrifying. I did well last time, so the pressure is on to prove it was the norm and not a fluke. Obviously, I have amazing self confidence. I went ahead and started making a frame work for my presentation. I want time to thoroughly practice and review it, but I also want to make sure I have a clear idea what results I need to focus on producing for the slides.
Okay, goals for next month: 1) use timer, 2) grade/ focus on astrobiology less, 3) spend time reviewing Titan, 4) work on presentation, and 5) produce the results needed for the timer.
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.
12/2/19 – Another Month
I came in this morning to find the 200 m depth python code I had running over the summer was still running. Unlike with MATLAB, I don’t know how to measure its progress. I am going to let it continue and when I need a figure I may have to use an existing result from the previous set up for the meeting on Thursday. In the meantime, I need to finalize the presentation and the annual report write up.
Goals: Work on the report and presentation over the next two days. I intend to have the written report done by EOB on Tuesday and the presentation by the end of Wednesday. The last couple days of the week, I will work on the manuscript edits.
Okay, so the annual progress report meeting with my committee was today. It was vicious. I’m writing this the following Monday, so luckily I’ve had time to let it all sink in. Nevertheless, I’ve got a ways to go. I am not prepared for comp exams in February and it is being pushed back until April or May. I do not have a sufficient understanding of how the code I am using works. Granted, I reviewed it at the start of the year, but after I got to Georgia Tech it became hands on. I made the necessary changes and everything after that was about getting the necessary results. In any case, this has been an eye opener.
Catherine, has given me some recommendations on how to try and improve my understanding of the novel (e.g. replicate pieces of it in Matlab). I’m working on that. Even on my first review, I recognize the discussion makes more sense this go around having been hands on with the model, so I am hopeful moving forward. I won’t pretend it wasn’t embarrassing and shameful to be told, “you are not at the point you should be at the stage in your PhD (~16 months in).” It was tough but necessary. I’m not about to give up. As long as I am offered a path forward I am going to take it, and I must say, I feel better despite what happened. Obviously, I’ve felt like I should be further along. It sucks to have that confirmed, but it means I have more guidance to get on track.
There was some criticism in regards to my Annual Progress Report. Apart of choosing not to pass it by Catherine first, I don’t regret how I approached it. There is literally one line even addressing the need for an Annual Progress Report on the Earth Sciences requirements page. I used the template I was given a couple years ago that asked for Background and Progress to date. I knew it was an abridged document and made a conscious decision to include references in text, in case the reader wanted to dig deeper, but this wasn’t my proposal. Therefore, I opted not to provide a full list or a complete run down of the model. I did the same thing for my first report.
Obviously, my lack of details on the model was representative of a greater problem, but it is frustrating that there aren’t more details on this provided by the department. I recognize this may have been resolved, at least in part, if I had reached out and included Catherine in the process. Unfortunately, I wrongly presumed to think that wasn’t necessary because I had been through the process before. I am trying to make a point to reach out to her more often.
I’ve taken to using the tomato timer. It has helped me focus a good bit, but I’m also faced with quantifying all the time I could be working. I can fit 15 pomodoro’s in an 8 hour day. Of course, things come up, so my goal is at least 10. I have yet to achieve this. I spent a good deal of time studying the model and making notes/writings in my proposal. Unfortunately, I lost focus later in the day Monday. Then Tuesday didn’t go much better. In any case, I think it is a good thing to work towards. my tasks/goals: continue studying model/editing proposal, edit manuscript, work on LPSC abstract, and a bunch of administrative tasks.
One thing I think might help to keep me focused. If I get the urge to do something distracting, I can log it as a personal pomodoro. While still a distraction, hopefully this will help me regain focus after the 25 minute segment is up.
I’m still getting the hang of using the Pomodoro timer. That is to say, I am not reaching my goal of 15 Pomodoro’s, but it does help me focus. Of course, things come up (meetings, problems and helping others). My minimum is 10 that I try to strive for. I have room for improvement, but I made good progress on reviewing the model. I’ve been doing a lot more back reading. I haven’t applied any of it to MATLAB yet; I am trying to review the different models the Planetary Ice Model (Buffo et al. 2019) builds on. I am getting a much better senses of the assumptions I have to make here and how the code works in general. In regards to my LPSC abstract, I’m roughly half way through it which I feel good about.
I’m still spending a good deal of time reviewing the model. As I do so, I am finding which assumptions are being made where. I haven’t started trying to replicate the code yet. I think what I might do is use what I have, making note of what assumptions are where such that I can return to them later while still getting along with doing hands on work with the code.
I’ve been trying to get a good figure for my LPSC abstract. That means I’ve been frantically trying to get the analytical fits to work with the model results I have but have to get more results each time. I have a final exam tomorrow to proctor (and start grading), and I am beginning to worry about my abstract because I really wanted this done today with the exam the next couple days then traveling home on Thursday.
I finished the grading. I ended up staying up late last night to get it done, but it left me with time to finish packing. I leave tonight at ~3 AM. I think I should have time to finish my LPSC abstract by Friday, and I am hoping I can get my manuscript finished by Monday.
Its proven much harder to get the work done. Family get together over the weekend didn’t leave a lot of down time. Then, yesterday, my computer crashed, so I’m using my iPad and an old laptop with a broken key board. Imagine typing with an on screen keyboard (not a touchscreen). I’m working on the abstract and should be done by the end of the day. The manuscript is taking longer than I would like. It will likely be Friday before I get it done.
I got the updates back and am working on those for the LPSC abstract. I finished the updates on my manuscript (a little later than I had hoped). Luckily, it was also not as bad as I was expecting (I just had less free time than I had hoped). I have this week to do the revision on the LPSC abstract. I can do that.
This has been a busy break. I’ve barely done any reading let alone blogging about my reading, so I’m ready to get these edits done so I can finally do a bit of that 😊. Even these updates, I’m making them in the new year based on memory because I just haven’t had time for it. Luckily, things are beginning to lighten up. It’s a new decade and a new year. I’m excited. Its a big year (comps) of my PhD and hopefully of reading. I’ve got a reading goal of a 100 books, and that’s fairly conservative considering the pace I’ve been reading at. Be sure to check out my end of year stats post for the books I read last year (still in progress)!
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.
11/4/19 – Another Month
I’ve made a lot of progress in regards to grading of the midterm in Earth Rocks. I spent a good deal of time over the weekend to make sure I was finished today. I have another 8 to grade (maybe a few more after this), but the bulk of it is done. Today, I’m working on creating a code to visualize the results the 2D model is giving. I need to compare the results I am getting for different inputs as I finalize the conditions for HCN. I’m struggling because I don’t know how to use the result data file, .pkl. I think I will reach out to someone who knows Python because I fear there isn’t a simple solution.
I hope to finish this tomorrow if not today. I am in the meantime trying to run a few codes for the melt ponds at 10s of meters at a finer resolution to see if we can have slightly higher resolution for instances of drainage. Right now, I am running at 0.01 m starting depth and at 0.1 cm increments. It seems to be working for ppts at 100, 500, 750, and 1000 at 1 second time steps. That is very slow, but all I’m looking for is low depth results (~10m).
I got the email for my revisions today. They shouldn’t be too drastic, but I only have a month. I noticed when trying to resubmit a revised paper, the Cassini Special Issue is no longer an option. I can only assume that I am too late for that. I didn’t realize I’d be penalized for the review process taking the time it took. I suppose it doesn’t really matter in which edition it gets published, but it is disheartening nonetheless. It would have been nice to see my work in the final review of Cassini work.
This has not been a great week. It’s so easy to keep pushing off discussing my progress until I feel like I have something substantial to say, but I don’t think that’s productive. I finished grading midterms, but that didn’t take all week. I helped Gavin and Carol with a couple things. Of course, that only took a few hours at best. I reviewed my feedback from the reviewers on my paper, and I spent a bit of time checking and changing the planetary ice MATLAB code. I got some aid from Chase on how to use the results the 2D heat transfer model, but I’ve yet to do anything with it. I can talk about little things I did, but the crux of it is I could have done better.
It was a week of distractions and procrastination. My goal is to shame myself into avoiding letting this happen again by talking about it here. I will say, I’ve gotten better at staying off Facebook. That was a serious problem for a while, but I’ve made a point to simply avoid the most distracting (online games) aspects while working by avoiding it outside of work too. That doesn’t mean there aren’t other distractions too. One thing I’ll try doing moving forward with this blog is start by setting up goals before each day to help me focus.
Goals: Begin reviewing the notes Chase sent me. I need to read through it and set up a template file or framework of troubleshooting. I don’t have to get it working, but I need to at least have something that should be outputting/visualizing results. Lastly, I will spend 2 hours working on my manuscript edits.
Results: Success! Or at least partial success. I still have to create a code to plot the results, but I figured out how to load and save the ‘.pkl’ results as a ‘.mat’ file. Chase provided me with a fantastic walk through of how to deal with the results. I haven’t gone through the entire example he provided; it loads and plots the results in Python. Once I figured out how to load the data, I was able to Google how to convert it a ‘.mat’ file.
Note for self: this is saved as a python code called ‘trouble.py’
I was mistaken when I read that the paper was due in early December. I think that was when they wanted me to decide on if I wanted to resubmit it. It is due January 3rd now, but I still want to try and deal with it sooner rather than later. I started the edits. My “2-hour” window was a good motivator, but I did get distracted there a few times. Overall, I still think it was a successful approach. I’ve begun by addressing individual comments based on those that seem easiest to address. These are minor changes, and even those that are more significant have room for some pushback.
One said change is a request for a traditional crater size-frequency distribution. I don’t hate the idea of this, but I dread the amount of work it will take because I need to learn how these are formed. I’ve attached an example here. I assume the cumulative frequency is the crater count and the area then is either the area of a crater of that size, the total area covered given the number of craters that size, or the area of the region (planet) being studied.
Other then the work I had planned, I met with the Space Grad Council.
Goals: With the data uploaded to MATLAB, the next step with dealing with the 2D heat transfer model results will be using the data in MATLAB. My goal is to finish reviewing the example Chase has provided me with; I expect it to be a fairly quick process since I’ll be doing in MATLAB. This should be done at the latest by the end of Wednesday. On Tuesday and Thursday, I will spend at least 2 hours working on the proposal (each day). I will spend at least 2 hours (total) editing the manuscript over the next two days. I’ve also got lab and will spend a bit of time preparing for that.
Results: I figured out how to export the results into a MATLAB compatible ‘.mat’ file, and I easily made a few graphs from it. That leads me to the final step of finalizing the chemistry parameters for Titan now that I have the size and Temperatures working and the results plotted (I’ll work on sharing an example here). Unfortunately, writing was not so successful. I spent a maybe half an hour working on my proposal, not enough, and I didn’t get around to working on the edits. Granted, I had lab Tuesday afternoon and again Wednesday afternoon, but I could have done better.
With lab, I have to change focus to grading for a few days. That’s the goal until its finished. I feel confident I can finish these by Tuesday.
Goals: My goal is to be done with these by Tuesday. I need to load the Wednesday labs (or some of them) and grade my part of the three Thursday sections. I also realized I still need to catch up on some of the TEPs seminar’s I’ve missed. My goal is to watch them (there are only a few I think) while I grade because it the labs are easy enough to grade without requiring too much thought.
Result: Grading has gone well! I have loaded all the Wednesday sections (that I have), and I’ve graded 2 out of the three Thursday sections. The 3rd one is the smallest of the three, so I feel confident that I will get through it tomorrow (probably with time to spare).
Results: I finished all the grading on Tuesday as I hoped I would. I did not get the TEPS videos yet. I really just need to have the play while I work. It will be the quickest way possible. I didn’t set any hard goals for myself today. However, I spent time working with the 2D code to figure out the final inputs to make. I need a clear plan moving forward.
Goal: I don’t have a hard goal set for the TEP; it still isn’t a priority. I’m at the point where I need to 1) input the 1D concentration model results into the 2D model. This means use the data I have and fit it to the concentration fit curves that Jacob et al. 2018 outlined. Then 2) figure out how to adjust the lens shape to be a cylinder. I need 1) done by the end of the day Friday, and I want to contact Chase about 2) tomorrow; that shouldn’t be a massive change.
This is important because I want to have a 2D model result in my proposal and for my December 5th meeting (at 2PM) with my committee. Which, I don’t know if I mentioned I finalized that meeting as well. Of course, I don’t want to leave my proposal writing unattended, but rather than set a time limit, I’m going to make it a content one. I need each section outlined to have a rough outline of the content I will discuss there beyond the titles I have created, including tables and figures where applicable. Again, this is by the EOB on Friday. This is a clear goal that can be met regardless of if I get distracted.
Results: I’ve condensed all of my concentration data into a file, but I still need to trim the anomalous data and fit it to the curve. This goal was a disaster and a major let down. I did not make progress on the proposal. I got distracted by having to collect and organize the Astrobiology documents for the new Astro professor. At least that is pretty much done. Then Thursday, I lost a big chunk of time helping someone with a MATLAB problem.
Goals: I am adjusting these goals. I will have these fits finished by EOB on Tuesday. Wednesday, I will try and produce results using these fits. Thursday and Friday will be proposal writing. I am also going to find times to watch these seminars. I need to think about the Manuscript as well. I will reassess my progress on Tuesday and decide where to go from there.
Results: It is taking a lot more time than I would like to fit this data. I have the fit ready, but the filtering takes time. I wasn’t prepared for it (with a code ready). If you recall, the model is freezing 100s of meters of water into ice, and it is doing it on a centimeter scale. This takes a lot of time. To speed it up, I run the model at 10 m segments throughout the water depth. The trick is, it takes time for the model to “calibrate”. Essentially, we can see the concentration changing drastically as it levels into the actual concentration. At deeper depths, where the thermal gradient barely changes, this equates to a sharp increase then a leveling off that we would expect at these low depths.
I finished the fit, but now I am faced with a new problem. The fits don’t fit my data appropriately. These fits are the constitutive equation Buffo et al (2019) uses to show the model output is following what we would expect. We are getting higher concentrations than expected, but I think a big part of this is needing more data. The higher concentrations have been difficult to run, and I now recognize where the gaps need to be filled. I am working on running those, but in the mean time, I going to use the data I have to run the code to run the 2D heat transfer model. This process of trimming the data was tedious, but the code is now there to do use with ease in the future.
In other news, I successfully watched all the TEPS seminars I missed, and emailed them to confirm I had done it. Then I spent a big chunk of time finalizing my expense report for the cash advance I got over the summer. I don’t know why, but these reports are some of the most stressful things about grad school. I’m not usually a very anxious person, but this is an area where it happens. The result, I procrastinate it as long as possible. Even now, there are tedious forms and revisions needed; these are the very things I dreaded.
Goals: My committee meeting is fast approaching. I am going to begin working on my presentation for that and use my proposal as a framework to go by (and vice versa). I need to finish the expense report updates and go to research forum. Then I will focus on the python code. I need a result. That means plug in these model parameters, and then change the shape of the lens. The shape may be postponed if it proves too difficult. I have to look at my manuscript revisions next week too; I can’t keep pushing that off. I think I will try and fit work in Saturday or Sunday, but I have a lot to do at home which may prevent me. We’re in the endgame now.
11/29/19 Updating 2D heat transfer model and fixing expense report
Results: I mad a few updates to the expense report, and it should be good to go now. I logged in the concentration data (as it stands) into Python. These are just constants that are found in the constitutive equations Buffo et al. (2019) discusses) because our results should be following those very equations. As I said, they aren’t, at least not entirely.
Some equations fit for some of the concentrations, and like I said, I am working on getting more data where necessary to improve these results. The other constants needing to be changed are those used to define the eutectic (melting temperature of water by HCN concentration). The model assumed a 2nd order polynomial would work, but I upped it to 9th order for a more precise fit. Here is a figure showing those results; I won’t (and haven’t) posted many figures of these results because it isn’t my code. Therefore, I am trying to limit the amount of results I show.
Then, I realized the shape was already defined as an option in the code (thanks Chase!). I’m letting it run for a 80 km crater over 200 m depth, but with a grid size of 10 m along the depth and 100 m along the radius of the crater. I want to shrink these values, but I need to run the code on a faster computer to do that. I’m happy with this progress, even if it took longer than I’d have liked. Until Monday, I may just let it go, let it go, and watch Frozen.
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.
10/2/19 – Month to date
I’ve been looking into the melt pond sizes to try and approximate the appropriate size. To be honest, I am at a stand still. I started by wanting to compare melt sheets assuming a cylinder verse a partial sphere. After a while testing that, it wasn’t giving reasonable answers. Then, assuming a cylinder, it just becomes the depth of the melt pond at a given melt fraction is just the same fraction of the depth of the crater (assuming the final crater depth is comparable to that of the transient crater depth). That means a crater melt sheet on the order of 10’s of meters, not 100s of meters that is observed in O’Brien et al. (2005). Even when I use Bray et al. (2012)’s trend equation for crater floor diameter, it only starts to show results approaching O’Brien’s at 10% concentration (~200m compared to ~40m and 100m). Right now, I am just going to move forward and assume 200m deep with a width defined by the floor diameter defined in Bray et al. (2012). Return to Calendar.
10/7/19 – The Institute Launch and things
Last week, I put together a couple lego rovers for the launch of the Western Space Institute. Thursday, I didn’t make much progress with research because I had to sub for two lab sections which took up a good deal of my day.
Today, I attended the launch of the institute, but before I spent some time fiddling with the code. I decided to use the trend equation defined in Bray et al. (2012) for the floor diameter of a crater of a given diameter to figure out the diameter of the melt lens. With that, and an assumed volume for the melt lens, we can solve for the depth (or height h) of the melt lens. I proceeded to try and run the code to make sure my input would work. I am not familiar with the syntax, so I need to test it a bit to learn the ropes.
I realized I never tried to run the code. I figured out how to run it, and then came the errors. It appears I need the numpy package. I proceeded to install it and got a bunch of problems. I downloaded the package and tried to run it, but the setup failed. I tried other ways of doing it by going through some Homebrew program. I will give it a bit more time tomorrow then ask for help from someone with python experience. Return to Calendar.
10/11/19 Python updates and such
This week wasn’t as productive as I would have liked. I resolved the original issues I discussed before (with Jahnavi’s help of course). I was missing some basic packages like sets of functions in matlab that are required for scientific coding. I’ve fixed that, but I’ve also learned that the syntax is off in places because my python is out of date. I have conversed with Chase about it and am going to update my python to his exact version.
Beyond this, I don’t have much more to update. My Thursday was short because I went out on Wednesday night which was fun and relaxing. Return to Calendar.
10/16/19 – Holiday, Labs, and Python updates
Installing the new version of python was simple. It was getting PyCharm, the program I run python on, to register and use that version. I realized I needed to create a new virtual environment that used the updated version. It didn’t effect my codes, but it meant the couple of installations I did with numpy etc. needed to be redone. The process that I used for Python2 did not work for Python3 though. Rather than troubleshoot it to death, I decided to switch to a different python program, Anaconda. Ethan suggested it, mentioning most of the commonly used packages (e.g. numpy) come pre-installed. I also recall Jahanvi mentioning it as a common source. Hopefully, this will 1) make the existing syntax work without issue and 2) avoid having to install a 20 different packages, all the while trying to understand if its a missing package or another error. This is a slow but steady learning process that will improve my troubleshooting abilities in python.
In other news, my MAC restarted in the last couple days, so the running codes quit. It saves as it goes in case of computer crashes, but it’s an inconvenience non the less. I am going to look at the results I have now. After a while, it’s hard not to lose track of the system I had in place when dealing with 7 different MATLAB windows on two different machines. The main concern is 1000 and 750 ppt. 500 and down are running pretty smoothly, and they’re probably nearly complete. That is, they have data for the desired depth ranges.
Oh, I couldn’t possibly forget. Tomorrow I have a meeting with Nigel about Astrobiology beyond our initial introduction. I still need to prepare a folder of my electronic documents, but I also have the TA textbook and my printed slides with notes. In other news, check out my spookathon reading progress! Return to Calendar.
10/21/19 – Meetings and Coding
I had a couple meetings today. One was with Dr. Secco to discuss my thesis and him being on my committee. It went fine I think. I’ve continued fiddling with python. Its up and “running” in the sense that it seems compatible with my version of python. I’m now making changes to the code to figure out what works and what doesn’t. It seems like larger radii are messing it up, but I need to look into it more. I’m also reassessing my log of results from my Matlab code. I want to figure out what I have and what I don’t so I can focus my resources on the concentrations and depths that are most in need of data (the highest ones probably). I also need to move the codes to my laptop because Matlab crashed when I first ran the python code on the MAC. Return to Calendar.
10/23/19 Python and Proposal
I met with Dr. Pratt, and it went well. We discussed my project and my goals. I think the biggest take away is that I need to have a bench mark or bench test (what was the phrase?) to validate the reliability of my model. There are possible lab experiments that can be done. I am working through some ideas. On that note, I am working on my thesis proposal. I have a rough outline that I am working on completing, and one part of that are long term experiments that we can do. I need to discuss it with the team at GA Tech.
In regards to python, I have the original code up and running. I haven’t done anything with the results yet; I’ll probably start trying to put a visual code together next. I have made changes to the code (not all of them). Getting it up and running is still an accomplishment. I am running a couple of the changes I’ve made right now, and I am worried that the lateral size may be a computational issue. Its running for a while at a very high RAM. The Activity Monitor clocks it in at nearly 30GB, but this computer only has 8? My laptop has 16GB. This could be a serious problem. Nevertheless, I am hoping that if I change the depth from 250GB to a very shallow depth, it will take less RAM/time. Right now, I want to let it run and see if anything changes. If not, I’ll try lower depths. Then, worst case, I change the diameter to one the MAC can take, then prepare python on my laptop (or maybe even another lab) to run the code once its set up and ready.
I should also review O’Brien et al’s paper (and others) to make sure my assumption of melt diameter is correct. That is, I assume it is the diameter of the crater floor as seen on Ganymede craters (Bray et al., 2012). Return to Calendar.
The code crashed. It didn’t make it to the end. I assume it was the code that made it crash; the computer had restarted when I got back. That means I have to try some new spatial steps if I want to use radii as large as our craters (~80km). I think I mentioned I was going to reassess the matlab code to see which depths and concentrations I have results for. I haven’t gotten to it yet. They take time, and every minute I am not running them is a minute wasted. I will get to that ASAP!
This week I am co-leading Lab 5 for Earth Rocks. It’s structural Geology. I also am in the process of grading last weeks exams, so I don’t expect to make a lot of progress with my research. For the lab, I am a little nervous because structural is not really my forte. Tomorrow we also have the Space Grad Council pumpkin carving event which is beginning to feel little daunting with everything going on. Return to Calendar.
The pumpkin carving event was a great success! We even had parents bring kids; they were so cute!
Research wise, it looks like the python 2D heat transfer model is working with adjusted horizontal spatial steps. I think the next step is visualizing the results and making sure the parameters are adjusted to HCN. Then it’s just a matter of importing the concentration results from the 1D planetary ice model.
On that note, I got some codes running for 1000ppt (100%). These are lacking because they are so slow and prone to failing. I went very conservative and set it to run at 5 and 10 second intervals. I haven’t had time to check the others; I did 1000ppt (and one 750 ppt) because I know those are the worst off in needing data. I still want to figure out where I am standing. I may take up my colleague Brian’s offer to use one of his computers because they have very fast speeds. I believe they are Dr. Gerhard’s who is on my committee so it sort of make sense ☺️. Return to Calendar.
Days with an update link to the update below and are bolded.
Introduction – Restructuring my research update
If you’ve been following me, you may know that I have started reviewing books that I am reading. I am really enjoying this. I have spent less time watching TV and more time finding reasons to put on an audiobook. Then I spend so much time talking about things I loved or hate in a way that really helps me learn not only what I like but to understand why. Best of all, it isn’t that big of a time commitment because I only comment a bit here and there as I read and get things to say.
Now switch over to my research blogs, and these are often weeks (months lately) apart. Then when I do write them, I spend hours putting it together, collecting my thoughts and creating a narrative out of details that often allude me. Therefore, I am going to try a new approach. I will do daily (semi maybe) updates where I create a blurb about what I did that day. I am not sure how much I am going to like this. Especially since I have a serious fear of being found out that I don’t do enough work (spoilers). What better way to make that apparent than by giving a daily account. On brighter side, hopefully I can find I am working or at least improve upon the issue.
If this idea sticks, I will still try to do the occasional event write ups of big things. Of course, maybe I’ll find it less appealing in application than in theory.
9/18/19 – Month to date
Let’s get started! I should first recap my month to date. Late August I submit my revised manuscript. Right after I attend Dragon Con; in retrospect that might deserve a blog post. There were several interesting panels I attended. during Dragon Con, I set up multiple codes to run over the 5 days of fun. That ended up crashing, and I, idiotically, never planned any time for me to check in on the code.
I returned home on the third. I spent the following days troubleshooting the code. My goal was to streamline the process. The coding takes a lot of time. I am running over 7 different initial concentrations (10ppt to 1000ppt, or 1% to 100%). The process is speed up by doing modeling 10m at a range of depths (up to 300m) rather than modeling the entire ~300m (in a centimeter resolution). Another way to speed this up for deeper depths and higher concentrations is higher time steps.
The problem is the code breaks down. I set up a loop to reduce the time steps if it reaches a critical threshold and set it up to continue through the desired depths (1m to 300m). Initially, I think it failed with the time steps while I was at Dragon Con. I won’t get into the details. It runs now, but something is happening once it moves to the next depth where it calculates the initial thermal gradient then repeats over and over without end. Rather than get this to work, I have just resigned to manually moving it to the next depth each time. I keep fixing it, resetting all 7 models, then one inevitably reaches the problem first because the lower depths and concentrations go faster. At some point, I just have to say, it is doing what I want well enough, I can’t keep resetting the entire process, even if it isn’t 100% streamlined.
I did that between the 3rd and the 9th I think, but I probably should have accomplished more in that period. The 9th or 10th I moved onto fitting the data to the fits defined by Buffo et al. in his 2019 paper. After a little guidance from Chase Chivers in our last meeting before we left, I was able to use the fittype feature in MATLAB to set it up to find the right constants for the equations used to fit. I’d fit lines to data, but never before had I known how to make unique function like this, where I need multiple constants. To be clear, I did this with old data that I am now redoing. The point is, I have the code ready for when the data is processed. The 13th I had a TA meeting, and the intermediate days I was dealing with a variety of paperwork for things from when I was away. In retrospect, I don’t like not seeing anything substantial those couple days.
Monday the 16th I spent time preparing for lab this week which I am one of the lead TAs responsible for presenting the information and grading the labs. Yesterday, the 17th I TAed a lab section, and spent a while on the phone with CRS. I also spent the last couple days researching Richard Secco and other professors for my committee. I need to stop by his office as I finally got a response from him via email. I contacted Dr. Molnar about the same thing. She was open to it but questions whether she had the right skills for my project. I haven’t responded yet because I don’t know how. This entire process is a lot to handle. I don’t know if I should just say, no I think you would work well or if I ought to dig through the variety of professors in Earth Sci and on campus. This becomes a question of my project as a whole. How much will be composed by this project? Will it grow; there are ways. In which case should be talking to chemists? If so, is that really the road I should be going down? I wish I had more to show, but I suppose this isn’t such a bad thing to be thinking about. My comps is a matter of months away.
All the while, I am still monitoring my code, keeping it going. Literally as I speak, I have to stop because a couple codes on my mac did something they shouldn’t (running deeper depths on mac and shallower depths on my pc). I’m having issue with concentrations 50% and above because the code doesn’t want to work for large time stamps, so it ends up with 10s intervals, and these 10 meter sections take hundreds of years. Return to Calendar.
9/18/19 – Day of update
I’m back! You may think I wrote this continuously, but I got seriously sidetracked about the very thing I was writing about where my code really did not want to cooperate. Honestly, these problems aren’t that common. Last issue was a week ago, and the only problem I had here was transitioning to the next depth. Nothing was lost, just a bump in the road. That took up a bit of my afternoon today. I also spent ~45 minutes introducing labs to Lab 1. This is not a regular occurrence. I introduce and grade 2 labs for the semester. All the others I just have to proctor Tuesday afternoon and Wednesday evening (two sections of the 5 or 6 for the course). The rest of my time was mostly spent writing this pretty lengthy catch up. FYI, I advise you to check out the calendar at the top which I am linking to each date as I post it. This will save you from scrolling moving forward, and if it isn’t linked, assume there wasn’t an update. Return to Calendar.
9/20/19 – Grading and Distractions
The last couple days of the week I’ve spent grading ~120 labs or so. To be honest, I had a lot of struggle staying focused on the actual grading which slowed me down. I’m actually writing this the 19th because I know tomorrow will be spent grading as well. We have the Friday research talks, and any grading I don’t finish tomorrow will be done over the weekend. So end the end here, my procrastination only leads to more stressful weekend. Luckily, there will only be 3 other times this semester I have to worry about grading (2 sets of exams and one more lab). Monday, I will begin working on the python code. It has to happen because this is a magical blog where everything I write becomes reality (or is maybe that’s a curse?). Just you wait. Return to Calendar.
9/24/19 – Finish grading, wait no, theres more.
Things have not gone as I hoped. I didn’t get grading done over the weekend, but I pushed through it yesterday, up until 2am grading, at times resting my head to regain focus. Of course, I slept in a bit today in reward then came to school to log the grades before lab. After, I had intended to finally sit down with the code. Much to my despair, the labs I graded were only about 2/3 of the whole. I realized, as I sought the pile of labs for todays lab section, that I had put those in my draw here in the lab. 3/4 the sections I was grading were on Wednesday. I graded every lab for Wednesday, a task that was far more time consuming than I imagined, and now I am left with today’s section. Not only will it be unfinished for today’s lab, I will be working into the night yet again, but I swear to god I will get it done before I go to sleep. I really hate grading. The teaching isn’t so bad, fun even, but the grading is pure hell. I’d still rather get it done in binges than spread out over the semester.
I finished grading the labs around 7, but I had to upload the grades which also included added up the scores. This took time, and I continued doing it once I got home for 2 of the other 3 labs. I still need to load the grades for the 3:30PM lab tomorrow (my lab), but I will do that tomorrow. They’re already alphabetized for ease of upload. I count this as being done though, so success. That makes 4 workdays dedicated to grading, for better or worse. Return to Calendar.
9/26/19 – Emails and getting into the code
I spent Wednesday going through emails and taking care of some administration stuff. In particular, I went though the own your future program and registered for a number of workshops over the next 6 months or so. Unfortunately, I was limited this semester by TA obligations on Tuesdays. The last half of my day was spent TAing and preparing. I finally sat down to get into the python code Thursday. I updated my Xcode and began going through the notes I made with Chase to adapt his 2D code to Titan.
This code takes the results of Jacobs model, and recognizes what concentrations will be stuck in any point depending on the conditions (initial salinity, thermal gradient) when it freezes. The model assumes a well mixed pond and no horizontal mass transfer. The changes are not major and are mostly to do with parameters. I’ve spent the day looking through the literature to find the right values.
9/30/19 – Researching parameters
I have not gotten deep into the code itself. Rather, I am updating the basic parameters to fit Titan conditions. I will go through my logic here for feedback and to reference later. I am using a depth of emplacement of 1cm, but this may change. I intend to set up a meeting with Chase to discuss this again because there are some complications with modeling the boundaries. I use a surface temperature of 94K (as opposed to 95 used by Neish et al. (2006), but I am not too concerned about that. The more problematic piece is the basal temperature.
I am unsure about the temperature at at the bottom of Titan’s upper ice shelf. Mitri and Showman (2008) have a plot (Figure 4) showing basal temperatures for given grain sizes and ammonia concentrations. They show a range of 0-15%, so I assume 5% (~middle) for a grain size of 0.1mm because this is what they used to test convection. This gives a value of ~220K. 15% concentration goes off the plot but eyeballing it suggests ~140K. Neish et al. (2006) use T=176K for the ammonia hydrate when modeling a cryovolcano. If one assumes this is from the ocean (as opposed to a melt lens), I could use this to assume the basal temperature is 176K. The purpose of the basal temperature is to establish a thermal gradient in the ice shelf. For now I am assuming 176K to be conservative. I could use some advice on what is best or other sources to check out. I looked over Nimmo and Bills (2008), Tobie et al. (2005), Grasset and Sotin (1996), and Grasset et al. (2000). In the end, Mitri and Showman (2008) seemed like the best source.
Most of my day today (30th) has been spent investigating Titan crater melt formation (O’Brien et al., 2005; Neish et al., 2006; Artemieva and Lunine, 2003). Right now I have a thickness of 250m set in the code, but I know I need better logic there. Artemieva and Lunine (2003) give a conservative estimate of 2-5% melt in a crater 10-15km in size. O’Brien et al. (2005) uses terrestrial knowledge about the change in crater melt with size to scale this up to 5-10% melt for a crater 150km in size. Their logic is that the value may differ, but the basic function that controls crater melt production (i.e. increasing with radius, R^3). A key part of Artemieva and Lunine (2003)’s process was accounting for melt loss at the rims and to the atmosphere. Bigger may produce more melt, but as the depths begin to decrease, more melt may be lost. Regardless, I am going to work on a code to produce a range of melt lens for 2%, 5%, and 10% to see how significantly this effects the melt width and depth. This shouldn’t be too difficult because I need to do this to get constraints anyway, and all I have to do is run it for different melt fractions. I’d also like to return to this to do a more in depth post on crater melt production because it is something I will need to discuss in my thesis later on.
Picture it, Atlanta 2019. Here I am, working with my old research group at Georgia Tech in the Planetary Habitability and Technology Lab. It is quite the change from London, Ontario. The temperature alone is roughly 10 degrees hotter on average (5 in C). Returning to Western campus will be far more comfortable, but that will soon turn uncomfortably cold. Then there’s the city. Everywhere you look theirs something to do. Great food is in abundance (hence the ~5 pounds I’ve gained while I’m here), and there is infrastructure for biking.
Even with the unbearable heat, I take my bike to the old town beltline-trail, and I ride till I can’t no more. I got my water in the bag, bike bags are attached. stickers on my Black helmet with black tennis shoes to match. Can’t nobody tell me nothin’.
There’s also the distance. Its been great seeing friends and family. I went to some fresh water springs last weekend with my sister, father and a couple step siblings. I also spent my sisters 30th birthday with her and her friends at Myrtle Beach in South Carolina. I spent 4th of July with my dad at his house in South GA near Jacksonville. I visited a few friends and my mom a couple times over the summer too; they’re just an hour north east of Atlanta. I also got to see my grand mother and grand father in Macon!
Then there’s Werewolf ATL. It was great seeing all my werewolf friends in Atlanta. I was able to join in on their monthly WW meet ups and a couple birthday parties too! That has all be a blast, but the best is yet to come. Dragon Con is upon’s us. It is the superbowl for WW (in my opinion). We will be doing pregaming the Saturday and Wednesday leading up to it. (This all may have passed by the time I publish this post). This year I am volunteering and will enjoy moderating games for part of my time. This year, I have a strict schedule for myself to ensure I get a few hours of sleep (most of the nights), but I also want to make sure I diversify my time at DragonCon. There is so much more to DC than WW.
My first year at DC was dedicated entirely to Space, Science, and Skepticism tracks with a special focus on Space Track. This is where I first saw Dr. Trina Ray talk about the wonderful Cassini mission and how it had been officially extended. It was here that I chose to change focus and give space science a shot. Sure, I had years of love for space and science that had been culminating up to this point, but the space track is what did it, introducing me to people who work in the field. What’s more, it showed me just how much planetary science was left to be done. I must stop or this will become a love fest for space and science and so on.
My point is there are other things that are worthy of my attention. There are also other geek tracks that focus on science fiction and fantasy in tv, film, and literature. I have so much passion for the things I consume, and I have no doubt I would love these panels if I just made a point to attend.
That will conclude my trip as I return right after it ends on Tuesday, the 3rd of September. Then it’s back to reality.
New readers may want to check out my previous discussions on what I have been working on. I don’t have the pretty pictures I would like just yet. I have been modeling Titan impact craters with a mix of HCN and water for a range of concentrations to hundreds of meters in depth. The goal has been to find the concentration of HCN in the ice after it freezes assuming an initial concentration. We find this at a range of thermal gradients (depths), and this is all we need to do a 2D model for a melt lens of a given shape and size. Then, we can track the thermal gradient at each point in the pond and get a clear picture of the distribution of concentrations within the ice.
I have the concentrations. I need to fit it to a series of functions to plug into Chase’s model. We have discussed what I need to do to adjust it for Titan. I have not had a chance to do that yet. Once it is set up, we can run it. This is work I am trying to get started on. With the end of my trip and my impending manuscript deadline (I haven’t mentioned that have I?) I haven’t had a chance to dig into that yet. This is work I intend to get into this as soon as I get back. However, the actual results are still several weeks away because I identified a problem with my data. I have enough data to work with the model and get it set up (the hardest part), but the data I have is bad.
I made a mistake in the eutectic curve I used in the model that determines the HCN concentrations. This curve essentially says, if the concentration of HCN is X, the melting temperature is Y. The problem was that I mistakenly type 7307 when I meant to put 73.7. How I missed this is beyond me, but suffice it to say, it probably skewed parts of the data. That means I need to rerun my results. This isn’t all bad. I have a better idea how to expedite this process and can adjust a few of my input parameters. It will still take a few weeks to get the data I need because modeling centimeters in a profile of 100s of meters is tedious work.
But fear not! There is a clear path forward, and I still see myself on track to finish this this fall. That paves the way for the daunting task of where to go from there! I’m not scared. Why would I be afraid of reaching a point with no clear path forward (*sarcasm*).
I have finished making the updates for my manuscript. I haven’t done a lot of blogging about my work because when I wasn’t blogging, I was editing the manuscript. Forgive me if I was not too keen to carry over my thoughts to here (although you can enjoy my recent writings on books I’ve been reading). I sent my edits to my coauthors. I hope there aren’t too many complaints; the deadline is right at the start of September. The comments weren’t too extreme, but they did prove time intensive. There were changes I might could have justified not doing which would have saved me time, but it was hard to ignore it if I knew it could be done slightly better. Some of the more tedious tasks (table and figure updates) even gave me a chance to enjoy some audiobooks while I worked.
IT: Chapter 2
Finally, in what is undoubtedly the most important event of our lifetime, IT: Chapter 2 is set to release on September 6th. As sad I am to leave Atlanta, I am so excite to finally see IT: Chapter 2. It was such a blessing when the first was released a couple years ago, and I am so happy to see such a major motion picture production for one of my favorite books of all time.
I may update this with some post Dragon Con pictures and comments, but for now, I am going to sign off until I’m back beyond the wall.
Atlanta is hot. I made the mistake of biking in 30+ C (~90F) weather, and I thought I was about to die. Of course, I was probably closer to death when I left to to school one day and almost got hit by a car turning left only a few hundred meters from where I’m staying. Luckily, I just very nearly avoided the injury, and it prompted me to get temporary health insurance while I am here.
Oddly enough, I still prefer biking here than London, ON. The drivers here are rude, selfish, and dangerous, but there is still an awesome biking infrastructure. Before I moved to Atlanta, nearly 3 miles of the 6.5 mile ride had a dedicated pedestrian/bike path away from the street. That has now extended to ~4 miles. Its relaxing and a lot of fun.
Of course, all this is possible because I decided to buy a cheap used bike on Facebook market. That process was easy enough, but a used bike has issues that have been a real hassle to deal with. Nevertheless, I make it work. I really don’t like busing, and I didn’t budget to drive a car down and bring my bike (I probably should have). On top of biking, I got a gym membership at GA Techs Rec center. As an alumni, it wasn’t too expensive. I’m also having a great time catching up with friends, and the summer is still just beginning (even though its already June!).
Now onto research. For those who don’t remember, II am working directly with scientists at Georgia Tech over the summer. I am learning to use models they’ve developed and adapting these for use on Titan. To recap what I am doing: the goal of this project is to study how the organic molecules on Titan will react as liquid water in melt ponds produced during impacts refreezes. This will be a helpful step in optimizing future Titan mission science by understanding the environment they intend to target. I am modeling the evolution of the freezing crater melt-ponds with organic impurities using the one-dimensional, two-phase, reactive transport model that Buffo et al. (2019) wrote for Europa, which was adapted from their work tracking sea ice (Buffo et al., 2018). I am working with Jacob, Dr. Britney Schmidt, and the rest of the GA Tech Planetary Habitability & Technology Lab Group. Through my collaboration, I’ll be modifying parameters in Jacob’s model to meet the conditions I am studying, and adding the ability to handle more organic molecules.
I’m happy to say things are coming along nicely. Once I got here, Jacob was able to help me get familiar with his code very quickly. I can run example models of the liquid water refreezing over a given amount of time and make changes as needed. I modified it to allow it to run over a set depth rather than a set period of time since I am working with crater melt ponds of a set size. The model works by solving the physics of freezing for a very small sliver of the ice-liquid interface. These increments are customized for the model to run efficiently. It essentially is modeling a meter at the ice-liquid interface. I start it 10m below the surface because the solutions break down for the extreme thermal gradients we would see at the surface-water interface. This shouldn’t really be a problem, since we can extrapolate curves to the surface once we know what the compositional gradients are like in the upper ice shell (and this works really well for other examples).
The way I am using the model is I set it to start 10m below the surface. Then the model tracks evolution of the melt water for a specific amount of time, all within a 1m system. This system is split into 1cm increments, calculating the structure and composition for each 1 cm cross section within that 1m system. You can probably imagine how smaller increments or a larger system (than 1m) would be more computationally intensive. Luckily, the scales of problems we are interested in are meters to kilometers in size, so these results will easily resolve the top-level science we want to understand.
You may be thinking, why is a 1m system relevant for changes throughout the likely 100s of meters deep melt ponds? Well, the first meter is just the first step in the process. The model is set up to extract the results of each 1cm increment that is frozen over the set increment of time (100s) and then reruns the model for 1m below the now frozen section. We can do this because as it freezes, most impurities are rejected, but it takes time for the rejected material to mix back into the system. Therefore, we can see how after a particular time step, the concentration in the liquid fraction is highest near the top of the multiphase layer. At the same time further away, the concentration is still its initial value. Right now, I have the model chemistry set to conditions for salt in seawater (~3.4%). The initial concentration is something I need to consider in my work this summer; I’ll probably look into the mass estimates we see on Titan, or we may do order of magnitude investigations (1%, 10%). That isn’t a major priority just yet. Because the composition of the liquid below the doesn’t change quickly until a lot of the material refreezes, the effect of increased concentration as it freezes likely won’t become significant until the last few meters of the system.
That brings us to another complication with the model. The system is a top down approach. It doesn’t consider freezing from the bottom. For salts, Jacob does not think it should effect the top ice to add a bottom boundary considering terrestrial examples and since salty brines are heavy. We have to consider whether this will hold true for organics. HCN, and an HCN-Water mix is less dense than water and ice, so if the bottom freezes I wonder whether buoyancy effects would drive more impurities near the top over time. We think we may have a solution for this. However, it does complicate the situation.
The buoyancy of salt is what drives it out of the mushy ice as it freezes. If the salt is replaced with a less buoyant material (HCN), most of that material will just be frozen into the ice. Remember back to my last blog post; this is similar to what the organic material was observed to do in terrestrial lake ice (Santibáñez et al., 2019). Things become interesting is when we consider the bottom layer. Basically, the bottom layer is going to act like the top layer of a salt water ocean. As it rejects material, that buoyant material will mix with the upper ocean. Therefore, as the pond freezes, the upper ice will see increased levels of HCN frozen within it. Jacob’s model does not do well with negative buoyancy effects, but this does not undermine the effectiveness of using this model because it becomes applicable to the bottom layer where it can be thought to act in the same way as mushy layer in a salt ocean. We model the lower boundary, thereby finding the amount of material rejected. Buoyancy will mix it with the ocean. As it does so, it increases the net concentration and leads to increased freezing in the top layer that can be predicted using the results from the bottom model. The beauty of using this approach is that its based in terrestrial examples of volcanism which, unlike water, is less buoyant when liquid (Worster et al., 1990). I’ll make a point to come back to that to discuss it more detail later.
That covers the major assumptions and structure of the model, and progress I’ve made so far. Regarding parameters, I’ve successfully imported most of the expected chemistry values for HCN. I had some trouble finding its diffusivity in water, but Jacob helped direct me to a source that had it. I need to put together some figures that lay out the values, their sources, and any other relevant info. I’ll be presenting an Oral presentation next week at TEPS workshop in Toronto, so I’ll try and write that stuff up in a new post the week after. As I type, I’m running a 300m model using all these. It is taking a long time, but it should produce enough information to put together a presentation for next week and set up a plan for moving forward.
In other work, I’ve been making some updates to my glacier work. It is coming along nicely. We are basically preparing the results for a final write up of all the work we have been doing.
Let me begin with a brief research review. I went to Georgia presidents (family day?) weekend for Deceptacon. I had a tons of fun playing, moderating, and volunteering. While there, I took some time to stop by GA Tech to meet with my new collaborator, Jacob Buffo. We discussed the model, goals, expectations, etc. I took some time to talk to him about platelets. These are tiny flakes of ice that form in the suspended water when super-cooled water comes underneath the ice. It leads to these layers of platelets that are more porous (Figure 4).
I thought this sort of freezing may occur in Titan melt ponds, where freezing on the bottom may float to the top layer from buoyancy forces. However, Jacob didn’t think this was likely. Super-cooling plays an important part in this, and his work with melt ponds on Europa don’t show this. Furthermore, my initial interpretations that impurities in the ice were controlled by platelets was wrong. He is submitting a new paper on his melt pond work which I hope to write about more in depth later, but I can’t at the moment due to time and because it isn’t published yet.
I think the most interesting piece though is that there appears to be a relationship with the temperature gradient and the amount of salt in the ice. The result is that, deeper into a freezing melt pond the impurities drop off. This may introduce a problematic conclusion for Titan. Perhaps there will be substantial freezing in the ice, but it may be too close to the surface (freezing too fast).
One last thing I hope to discuss more is a paper, Santibáñez et al. (2019), that has only just been submitted about how bacteria and organic matter tend to freeze into ice much more effectively than inorganic material. This appears to be the case even for dead organics. This has the potential to be extremely important, because we aren’t dealing with salts on Titan. We are interested in the organics in the ice. I look forward to discussing this more at a later date.
CPSX Research Forum
I presented a couple weeks ago at the CPSX forum. I think it went well; I had good feedback. I was a little irked that there was such little turn out. Thanks to those that were able to make it though! The talk began by reviewing Titan and the reason it astrologically significant. I concluded that piece of the talk with a brief over view, of what it means to potentially have amino acids, and where that fits in the greater picture of life as we know it. I wanted to give perspective. I then continued by explaining how this was why Dragonfly has been proposed to go there. I then pivoted the talk to a more geologic one. I discussed Dr. Catherine Neish’s recent Astrobiology paper and how we can use impact craters to investigate for molecules on the surface (impact melt/water mixing with the organics). Then I used my master’s research to talk about how we can compare impact craters and identify the best candidates to search. I showed my depth to diameter plot before I introduced the large scale mechanics of how a impact melt pond would freeze. Then I explained how we can use rivers as a natural way digging in to find samples within the melt. I plugged my rim to diameter plot to illustrate how we can look for fluvial erosion (along with visual radar images). Then that was when I pivoted to the final stage of the talk, my newest project of investigating exactly how impurities would freeze in the melt. I think my worst part was the final part. It is the newest piece of my work, so it makes sense I would be less fluent in it. Nevertheless, I will need to practice that more next time.
The course is going well. I am enjoying it, and I can notice that I am retaining a lot more information than I did in previous years. We did the midterm. With it, came feedback. I was surprised that it was fairly positive. Only one person said it was unorganized. I got a lot of complaints about the tediousness of the labs. To be fair, some of them are ridiculously easy, and I wonder if they’d honestly rather have more complicated labs. Well, we are about to see because I’ve updated the habitability lab and made it a bit more complicated! Jahnavi was working through the lab, and she found a problem with the greenhouse/ albedo site that we use to calculate planet temperatures. When it came to including the greenhouse effect, the model wouldn’t update. See below, we give Planet X (the white circle) the albedo and greenhouse strength of Venus, but it gives a temperature half of what it should be. It adjusts for albedo, but different greenhouse strengths wouldn’t make a difference.
Therefore, I decided to restructure this part of the lab. Lets be realistic, this lab was so tedious and difficult to make work. Java was a hassle, and it really was not that exceptional of a program. Instead using it, we are now going to give them the equations and they are going to solve it. I still reference the UC module, and I even link to their planetary fact sheets. The difference is, they need to plug the values into the equation. It really isn’t that difficult, and it will help them get use to calculations in Excel before the Icy Moons Lab.
The math is simple, and if they are creative, they will figure out how to speed through the calculations. They can compare results, while flexing their problem solving techniques. In part B, I elaborate on the three factors that control the greenhouse strength 1) amount of atmosphere, 2) fraction of greenhouse gases, and 3) effectiveness of the greenhouse gases. I had to give (1) and (3) which I pulled from the online module, and the use the fact sheet for (2).
This also really cleans up the lab. The procedures were very tedious and crowded the page. Hopefully, this will be easier to navigate and more enjoyable.
I have lecturing pretty well figured out. I was behind due to the exam and the ice cancellations, but I have caught up. I think I may even move into next weeks material tomorrow. That said, I am worried that I spend too much time writing on the board. One student said what I was thinking, I write things that don’t need to be written. I am not about to stop. I want make sure I pace myself, and give them time to take in the info. I also don’t want to waste their time. I am trying to be cognizant of the problem to not over do it and to make sure I am focusing on the right things.
Updating other posts
In other news, I have updated my peanut cookie recipe. I finally have it down to a precise science. I’ve also updated my reading post with my February recap. Obviously, I spent time in my reading post discussing the television show Game of Thrones for whic the final season premiers VERY SOON!
I recently sent off my manuscript to the coauthors for review. Our goal is to finish up the final revisions to submit it in time for Icarus’ Special Cassini edition issue. I also received an offer to teach Astrobiology in the Winter 2019 term. Beyond that, have been granted funding to travel home (abroad) to Atlanta for the summer where I will work with my old adviser Dr. Britney Schmidt and her PhD student Jacob Buffo on a project I touched on in June 2018. Although, first I have to finish proctoring and grading for Earth Rocks this semester.
I have my work cut out for me, and I think we are the point where I’m in need of a good old timeline to set some goals for myself.
The manuscript has been sent to the coauthors. We have to make revisions to their suggestions. Then we have to send it to the Cassini team to repeat the process before the actual submission in January.
December 21st: Deadline for coauthors to return suggestions
January 1st: Deadline to send updated draft to Cassini RADAR Team
January 10th: Deadline for Cassini RADAR Team to return suggestions
January 10th-15th: Make final revisions and submit to Icarus
I applied to teach Astrobiology (I think a 3rd year course) in lieu of Catherine next semester. I got the offer (which I was expecting), so I can officially say I will be teaching it next semester. Catherine has generously offered me all her material for the lecture and labs. However, I still have to prepare for the lectures and decide if there are any changes I want to make. I suppose this all will seem obvious, but I think it’s necessary to approach this large problem step by step to avoid issues.
I have to organize the course material (Class site, etc.). Then create a timeline for the different subjects. I need to decide when lectures are covered and how to fit labs around them. The class project needs deadlines set up. These are all initial steps that need to be taken this month.
Even though I have the lectures, I need to sit down and develop my own approach for each lecture. That means, reading through each respective chapter and making sure I have an idea of what I am presenting it and how I want to communicate it. This is the most taxing thing I think. I need to begin this this month as soon as possible because I want to make sure I’m not falling behind with the course. Ideally, I’ll have 4 weeks (8 days) worth of material lined up, but I still need to make sure I have a clear plan on how to continue the process as the semester continues.
I have plans to change at least one of the labs. I need to get into contact with a professor at the University of Washington to get started. That may or may not happen, but I need to start working on that. With that in mind, I want to work through at least some of the labs to see if there is room for improvement. Particularly the one I helped make two years ago. I’d put these tasks as lower priority because what we have works, I’d just like to see if we can make it better. I’ll translate it to excel later.
Set up OWL (online site), make schedule, update syllabus, organize material from Catherine. Plan Project timeline.
Get in contact with Dr. Rory Barnes at UW!
Review First Lab: Lab 1: What is Life?
Set up meeting with Gavin to discuss first couple lab and course set up (he won’t be here until the day of lab that first week).
I could include the second TA, but I am not sure if it’s for sure.
Prepare lectures for Ch 1: Astrobiology and Life
Review Lab 2: Solvents for Life
Prepare lectures for Ch 3: Life’s Structure
Review Lab 3: Viking Labeled Release
Prepare lectures for Ch 5: Energy for Life
Review Lab 4: Titan’s primordial soup
January 7th-9th: Meet with 2nd TA
Prepare lectures for 1st half of Ch 6: The Tree of Life
Set up Outline to new lab
Do Lab 1; Ch1
Prepare for 2nd half of Ch 6: The Tree of Life
Develop Methods and Question for new lab
Do Lab 2; Ch3
Prepare lectures for Ch 7: The Limits of the Biospace
Complete/Troubleshoot lab; send to TAs to complete and make suggestions
Do Lab 3; Ch5
Prepare lectures for Ch 16: The Habitability of Planets
Do Lab 4; Ch11
Review Lab 5: Is it science?
Prepare lectures for Ch 17: The Astrobiology of Mars
Do Lab 5; Ch12
Review Lab 6: Tree of life
Prepare lectures for Ch 18: The Astrobiology of Icy Moons
Do Lab 6; Ch6p1
Prepare lectures for Ch 19: Exoplanets (Last Chapter)
I’m going to use some of the content I proposed this internship for background.
Dr. Schmidt and her team have been studying the Antarctic ice as an analogue for the Europa ice-ocean interface. Mr. Buffo has been developing a model of this boundary on Earth where it can be tested and validated, and then a few parameters are changed for application to the Europa environment. It follows the interactions between the salt impurities and the ice. One thing we see on Earth, is that even when the water-ice is pure, salty brine layers may still form within the ice. Dr. Schmidt, Mr. Buffo, and I are working to apply his model to Titan melt ponds to better understand how the organics will be collected in the ice. The biggest obstacle in applying this to Titan will be substituting Titan organics for the salty brines being modeled on Earth. It requires an understanding of their physical properties in water. Some assumptions will need to be made, but we believe this will help improve Dragonfly’s search for biomolecules on Titan.
I did a rough plan for the internship, which will extend between Monday May 13th, 2019 and Friday August 30th, 2019. chose the middle of May to allow ample time for finals to be completed and processed at both universities. The nearly 4-month internship is meant to provide abundant time for learning, troubleshooting, and application. I ended it in August because classes at Western University begin in September.
Below is a plan for while I am there.
2 weeks for troubleshooting issues I have understanding the existing model
2 weeks to familiarize myself with Mr. Buffo’s results
1 week discussing how we will go about applying the code to Titan
Titan atmospheric and melt pond environment
3 weeks implementing Titan specific molecules in the code
2 weeks troubleshooting using the new molecule
6 weeks to apply the molecule for different crater environments
2 weeks modeling 40km crater sized melt pond near the surface for non-draining ponds
4 weeks modeling ~80km crater sized melt pond near the surface (2 weeks) and near the middle of the melt pond (2 weeks) for a non-draining and draining ponds
That’s probably not new for Catherine, but for others it may be. It’s also nice to have it here to reference more easily. I still take it a step further, because May is a ways away and I need to begin looking at this more closely. Realistically, I’ll be tackling the very problems that are listed above, but nevertheless I’ll write out clear deadlines to strive for.
January 18th: Understand how the existing model works. Run, repeat, experiment. Review all available reading material.
February 1st: Understand the role of brines/salts vs organics. Understand what is required to substitute it and what out options are.
February 8th: Test the limits of the existing code. What can be changed. What it does to the system.
February 15th: Try regular code under Titan physical conditions (rather than composition).
March 29: Try a new molecule (HCN? vs salinity)
Find required chemical and physical inputs for molecule
may require some code based methods
Try testing it
April: With finals and projects, I’ll leave this free. Plus, if I make it to the March 29th step, I feel certain thats where I’ll need to sit down with Jacob to begin making the code work.
May: Take it from there to the list above.
Bonus: Crevasses in Greenland Glaciers
Several years ago, I submitted a paper for my undergraduate work with Dr. Schmidt mapping crevasses or fractures on Helheim glacier. This observational paper was rejected. Firstly, it was my first attempt and there is plenty of room for improvements writing wise, but more fundamentally, they needed more. They need use to analysis our results and to quantify them.
Dr. Catherine Walker, Britney’s one time post doc, was going to do modeling using them. I’m not sure where that went, but we wanted to get my work published as well. More specifically I want to. I began working on quantifying these results. I had hoped to get it done much sooner. That has not happened. There has been a lot of troubleshooting mixed with long bits of no progress do to other responsibilities by all parties involved. We have all tried to return our eyes to this to bring it to fruition. I have been working with undergraduate student Kathrine Udell who has done similar work to what I’ve done. Shes done other types of mapping in addition to fractures. I did not. However, I’ve worked to get results for my glacier, Helheim and for her’s, Kangerdlugssuaq Glacier.
I should take a step back and say, I’ve developed a code in matlab to quantify the maps. Katherine has helped me refine it to both improve our results and identify the best way to present the data. Presentation has been the biggest hurdle. Deciding how to talk about this type of data. This is already become more detailed than I intended, but long story short, I developed a grid to measure the fractures across the glacier. We’re looking at including orientation as well. This is a quick view of the most recent output.
I don’t want to get lost in the methodology, but the point is, we reaching our close. We don’t plan on working on this over the summer because we intend it to be submitted by then, so I need a plan. I need a plan that somehow gets me a paper with all I have ahead of me.
December 14: Outline of paper with major Figures and a clear idea of other figures left to make.
December 21: Finalize figures and send in depth outline to Britney, Catherine (Walker) and Katherine with a K (this has been my life for the last 2 years).
January 14th-25th (after Icarus paper is submitted): Methodology
January 28th-February 15th: Results
February 18th-28th: Introduction and conclusion.
March 1st: Send out for review.
I need to run these dates by them, but I like them and think its reasonable. Up to now, I haven’t done much with the paper. I’ve been so lost in the methodology; we have finally reached a point where we are comfortable with the approach we are using. Obviously, this is my lowest priority, but it’s something I need to think about. I’m glad I at least have something written out there.
Update: I’ve discussed this with my adviser, and I’m being too ambitious. I need to postpone this until the summer.
How long has it been? A while I’m sure, so let’s recap. Let’s start with last week. I went to bed last Sunday with a splitting headache. Was I dehydrated? I must have been for it to have been so bad. Come to find out the next day, I had a serious case of the flu. Barely able to get out of bed, I suffered miserably. It was probably the worst I’ve had it in years. Even when I tried to rest, I was miserable. Naturally, it made for a bad work week. I could barely manage enough energy to make food let alone work. I tried to TA Tuesday; that was a mistake. I didn’t stay long. Hopefully, none of the students got sick. I didn’t make the same mistake Thursday, but I was mildly better. Or rather, I had to be. I had an application that I had intended to do at the start of the week but was unable to do. Now I made myself do it. I submitted the application to work in Atlanta with Dr. Britney Schmidt and her student for about four months from mid May to the end of August. Hopefully, it gets accepted.
Prior to that, I visited Mexico with my mother and older sister on a cruise. I had a great time visiting with my family and exploring the underground river caves in Mexico. We also explored some awesome Mayan ruins as well.
For Halloween, I was Winifred Sanderson. My sister and her boyfriend were Tina and Gene from Bob’s Burgers (see cover photo).
I am applying to be the instructor for the course in Astrobiology. Lets hope I get the job. I don’t think I’ve mentioned, but there is an update happening to the Astrobiology Primer. The primer is a guide to learning and teaching leading concepts in astrobiology. I have signed up to help. It is still in its early stages. Most of the chapters have been developed, and we are decided on who will be the editors vs authors of chapters. I hope to help author parts of it. More to come later.
In other news, I got an updated draft of my manuscript to Catherine a few weeks ago, but there’s more to do there. That is my priority this week. I’ll add updates on this as things progress before our meeting Wednesday.
I’ve updated all of the figures so all is left is to deal with words for the next few days. That keeps me on track to update by the end of the week I think. Here is a quick review.
I updated my methods and results to include stereo data measured using a new method. I have to go back and make a few more changes. The way I discuss the results needs improving, but the figures are done like I said (at least for now). Work in progress.