3rd Joint Meeting 🧠
Sunday, September 28
158.7 lbs (from 165.4 lbs on Aug 24) | 🏃🏻 Done (7/6)
I took a yoga class, then went to the lab to set up the same amide coupling. This time I increased the equivalents of the coupling reagents per the SI. Since I don’t want to do an aqueous workup just to remove DMF, I’ll purify again by reversed-phase chromatography, but this time making sure to run with TFA🤨 If it still fails, I’ll follow the exact protocol: 8eq. of EDC/DMAP in DCM at 60 °C overnight (unusual conditions!).
The rest of the day, I did some work and prepared slides for tomorrow’s group meeting. For the next few sessions, the format has shifted from a single two-hour talk to several short updates. I’m not sure I’ll present, but preparing in advance is definitely the safer choice. I think the biggest benefit of preparing a talk is that it forces me to re-evaluate the strengths and weaknesses of my project. When I build a research presentation, I try to simplify the story and keep the focus on the “why” (while still covering the what and how). That process made me ask again why I’m doing this at all, and I realized how much I still need to prepare and learn. I finally wrapped up around 1 a.m. (it never ends) and went to bed.
Monday, September 29
158.0 lbs (from 165.4 lbs on Aug 24) | 🏃🏻 Done (1/6)
Even though I slept a bit late yesterday, I went to the gym. I considered skipping it, but I knew I would be in a better mood after a workout. Today was busy with a morning and an afternoon meeting. I went to the lab a little early to quench an overnight reaction and ran purification during the group meeting. I like the new meeting format, which is short updates instead of a single two-hour talk. By this format, more people get chances to present, which helps us organize progress and get feedback. I’m not confident with chalk-talks yet, but I need to do one for my qual, so it’s great news that second-years will get practice.
After the meeting, I checked the purification, but the product (which is not UV-active) never appeared in LC-MS, even after checking 40 fractions out of 80. I suspect the product is acid-labile (decyclization), so I’ll switch to normal-phase and use staining next time.
I grabbed a quick lunch and went to another lab to prepare for the afternoon meeting. I’m learning yeast surface display, and I’m lucky to work with a postdoc who did a lot of YSD in his PhD. Bill proposed a way to get more efficient library design, so another postdoc and I worked through it. The meeting went well; I’ll inspect the structure in PyMOL to finalize library size and diversity for my project.
After work, I attended a KOLIS seminar on structural biology. It was a bit advanced for an “introduction,” but still informative. I wrapped up the day by doing meal prep and making a few slides, since it wasn’t my turn to present today (and might not be next time either😅).
Tuesday, September 30
158.1 lbs (from 165.4 lbs on Aug 24) | 🏃🏻 Done (2/6)
Managed to work out, then focused on the yeast display library design. It took a while to choose the exact amino acids for each position, but with Bill’s intuition and a postdoc’s guidance I finalized a pilot YSD library. Exciting! After sending the design, I organized my progress and uploaded a progress report and pre-meeting notes for my PIs, since tomorrow is our third joint meeting. I’m always grateful to get an hour with both PIs each month, given how busy they are. To make the most of it, I am trying to prepare as thoroughly as possible.
Finally, one full computational protein design workflow is approaching the finish line (just one of many possibilities😛), and I’m starting to see promising signs…? that it might produce results. I will polish it and lay out the logic clearly before the next joint meeting. After work, I went for a run. Next time, maybe on the weekend, I want to practice running for more than an hour. The SF half marathon is still a ways off, and I plan to start formal training in February, but building a base now can only help. Back home, I had dinner and kept preparing for tomorrow’s meeting, and went to bed around 2 am…🫠
Wednesday, October 1
156.5 lbs (from 165.4 lbs on Aug 24) | 🏃🏻 Rest (2/6)
I usually go to the gym even when I sleep late, but today I had three meetings (group meeting—joint meeting—group meeting), so I rested🥹; I literally didn’t have time to review my materials. The morning meeting was in the DeGrado Lab. The speaker was my student mentor, a fellow CCB graduate student who is about to graduate, and it was nice to see a totally different angle on protein design.
I skipped lunch to prepare for the upcoming joint meeting, and it was worth it. The meeting went very well. Every time, both PIs encourage me to stay consistent and offer lots of positive feedback, which really recharges me. They also actively propose and refine ideas, and some of those suggestions genuinely shift the direction for the better. It still amazes me how endlessly creative they are at their career stage.
Right after that, I went to the Shokat Lab group meeting, where two third-years gave chalk talks (they passed quals only a few months ago🎉) and did an awesome job explaining their work without slides. They’re smart (and kind). Hope they get everything they’re aiming for in their PhD journeys. After work, I spent some time writing a post-meeting summary.
Thursday, October 2
157.1 lbs (from 165.4 lbs on Aug 24) | 🏃🏻 Done (3/6)
Leg day again. I suddenly realized my routine is heavily focused on glutes and hamstrings🧐 I used to include hack squats, but my current gym does not have one, so I stopped. I might try Smith machine squats instead?
Today was my first time seriously teaching someone a computational workflow. About a week ago, a Shokat lab graduate student asked me to walk her through running AlphaFold3 with a user-specific ligand and a covalent restraint on the protein of interest. She had not done much computation, so I prepared the simplest possible demo. After about two hours, she understood how to run it and how to repeat similar predictions on her own (but with many resources to see🙂). I realized I still need a lot of practice speaking English. When I try to say faster, my word order flips into Korean, which is often the opposite of English. I hope this improves with time.
After the demo I had lunch with a DeGrado lab graduate student who was the speaker from yesterday’s group meeting. She is also my student mentor and my journal club coach from the new student orientation. She helped me a lot in adapting to the lab, so it was nice to chat comfortably. Her recommendation for Publico’s Thursday special was spot on too.
In the afternoon, I spent time digesting everything from the joint meeting by writing a summary and sending action items for myself and for both PIs. It is satisfying to see progress since the last meeting objectively, and the weak or lagging parts become obvious in the document and email, which keeps me alert.
After work, I ran straight to Pier 39 (about forty minutes from Mission Bay) in perfect weather, not too cold and not hot at all. At Pier Market Seafood Restaurant (39 Pier, San Francisco, CA 94133), I ordered clam chowder (actually my first in the U.S., I had tried it once or twice only in Korea) and a fried platter. Considering it is the heart of a very touristy area, the price, service, and atmosphere were great. Next time, I want to try more spots along the way to Pier 39, because eating while looking out at the bay feels wonderful.
Friday, October 3
157.7 lbs (from 165.4 lbs on Aug 24) | 🏃🏻 Done (4/6)
I got a good workout in today, and since I finally had a weekday with no meetings, I dug into work. Because I am still new to dry lab work, every day brings new things to learn and factors to consider. What I first thought was “enough” keeps revealing holes; once I actually run things, I see the model’s limitations, the many choices at each branch point, and how those choices limit downstream steps. In the end, anything is fine if it gets me to the goal, but I still need the knowledge and reasoning to choose well, and that is not easy. A friend once said deep learning can’t find a true “optimum,” and I am starting to understand what that means. Even so, I want to try everything, step by step, until I can honestly say, “This is the best I can do.” There is a lot to do and new issues keep appearing, but I do feel I am making progress, so my mood is good.
I ate lunch with my cohort for the first time in a while (apparently we have to film a video for next month’s retreat…😵). I went back to work afterward. It turns out HPC storage was a bigger issue than I expected… so many things to consider🤨 After work, I went for a quick run and finally wrapped up this long weekday.
Saturday, October 4
158.8 lbs (from 165.4 lbs on Aug 24) | 🏃🏻 Done (5/6)
Another solid workout this morning (my yoga pass just ended, but the instructor returns in three weeks, so I’ll renew then), and I headed straight to the library. I really love the place. It is quiet, spacious, and somehow cozy; perfect for getting work done. I meant to write a blog post, but truth be told, I focused on my project instead… and then accidentally deleted an important script and spent a lot of time recovering it. Please use Git and back things up, please…
For dinner, I wanted to try crispy, skin-on pork belly in the air fryer, but it was surprisingly hard to find with the skin attached at Safeway, so I ended up going to Costco. It was tasty, but getting that extra crisp texture is harder than I expected. You really need to dry it in the fridge for a few days like in the YouTube videos. I ended up finishing it in a pan, which was decent. I’ll prepare better and try again next time (btw it’s a shame that I didn’t take a picture of the finished dish😅).
Oh, on the way from the library, I had a 20-minute transfer gap, so I went to Woodlands Market (203 Folsom St, San Francisco, CA 94105). It’s beautifully put together with tons of tempting items; I want to go back and browse again. Halloween is still a ways off, but lots of places are already stocked. There were some sooo cute decorations. So naturally, I looked up apartment prices nearby and… wow. The top floor was around 20 million. Even if you made 200 thousand a year, that’s a hundred years! I guess that level of wealth takes a business or something. Anyway, let’s focus on PhD😇
