Just Ordinary Days
Table of Contents
Sunday, May 4
166.8 lbs (Day 128, starting from 162.6 lbs on Dec 28) | 🏃🏻 Done (5/6) | ★★★★☆
I slept for about 8 hours, which felt like enough rest. I headed straight to the gym with my friend and did a quick upper body workout, followed by a refreshing swimming session. My goal is to increase the number of reps (one rep = one round trip across the pool) each time I swim. I’m now considering adding one more swim session during the week, in addition to the weekend. It gives me such a great feeling and it’s actually a really fun way to get in some aerobic exercise.
After getting back home, I started my proteomics assignment and wrote a bit for my blog. Then I headed out again around 3:30 PM to get a haircut in Chinatown. I had dinner plans at 5 PM with my current lab members at Japantown, so I timed everything accordingly.
The haircut turned out great, and dinner was decent too. Funny enough, it was my first time going to a Korean BBQ place in SF. I’d give the place a 3.5 out of 5. (YakiniQ Korean BBQ, 1640 Post St 2ND floor, San Francisco, CA 94115) After getting home, I finished and uploaded my blog post, did some more work on the assignment, and went to sleep soon after.
Monday, May 5
167.0 lbs (Day 129, starting from 162.6 lbs on Dec 28) | 🏃🏻 Done (1/6) | ★★★☆
Outside of Work
After class, nothing special happened. I just focused on my experiments. Since I couldn’t go to the gym in the morning, I rushed there right after work. The weather was unbelievably beautiful, so of course I headed to the rooftop. There, I ran into two of my cohort members. We worked out together for a bit and even played some basketball🏀 I do wish there were a more serious basketball club here, but honestly, just getting to play is fun enough. After getting back home, I had a late dinner, finished my blog post, and went to bed early.
Lab Work
Chemistry
- SJ-1-27A, B NMR
- SJ-1-30 NMR
- SJ-1-31 rxn, work-up
- SJ-1-32 rxn
- SJ-1-33 rxn
Tuesday, May 6
168.0 lbs (Day 130, starting from 162.6 lbs on Dec 28) | 🏃🏻 Done (2/6) | ★★★★
Outside of Work
I started my day with a refreshing morning workout. If everything goes as planned, this week will mark the end of my chemistry experiments—and I’ll finally be shifting into biology! It’s kind of unbelievable, but I still haven’t done any cell-based experiments. I haven’t even done a Western blot yet, which is almost a rite of passage in biology labs. Learning something new is always a bit nerve-wracking, but when I feel like it’s something I really need to know, I tend to stay focused and even find it fun. So, I’m looking forward to it! Though… whether the results will turn out well is a different question, haha.
After work, I had a delicious Korean meal (김치찌개; kimchi stew!) at a friend’s place. Their parents recently visited and cooked a bunch of Korean dishes before leaving—turns out they’re amazing cooks. It made me really miss my mom’s home-cooked meals.
Umm.. my travel request to visit Korea still hasn’t been approved yet. I honestly have no idea when I’ll get a definite answer on whether I can go or not. I still need the signed DS-2019 with the travel endorsement before I can leave, so I’m a bit worried. But since my visa is valid for two years, at least I won’t need to renew it right away. Fingers crossed I’ll be able to go!
Lab Work
Chemistry
- SJ-1-32 purification, NMR + repurification
- SJ-1-33 purification
- SJ-1-34 rxn
Wednesday, May 7
167.3 lbs (Day 131, starting from 162.6 lbs on Dec 28) | 🏃🏻 Done (3/6) | ★★★★☆
Outside of Work
I had a group meeting this morning, and today’s presenter was the only PhD student in the lab. I have to say, the PI gives incredibly detailed feedback. Sometimes it feels like he’s obsessing over the details—but honestly, I think it’s somewhat necessary. He not only pays close attention to the data but also provides thoughtful guidance on research direction. With that level of involvement, I don’t think we’ll ever get too far off track or fail to publish.
Group meetings are usually two hours long, but today it ran over two and a half hours… so yeah, it was a bit exhausting, haha. Toward the end, the PI suggested that we try predicting protein-ligand complex structures that our lab is interested in. So, I’m planning to explore the newly updated Boltz-1x model.
For lunch, I went to Moshi Moshi (2092 3rd St, San Francisco, CA 94107) with an adjunct faculty member from my first rotation (also a senior from my pharmacy school) and a Korean postdoc in the lab. I’ve been wrestling with lab decisions lately, so I asked them for advice. Their insights were super helpful. They also encouraged me to seriously consider co-mentorship, which I hadn’t thought about deeply before. Talking to people who’ve already been through this journey really broadened my perspective.
I wrapped up my experiments pretty quickly today and spent most of the afternoon figuring out how to run Boltz-1x on HPC. It’s a bit tricky since the installation is different from Chai-1 or AlphaFold3. I’m thinking of setting it up with a Conda environment like I did for Chai-1.
After work, I went to the gym with a friend. We had made a bet over the weekend about which set of stairs in the gym building had fewer steps (1st to 2nd floor vs. 2nd to 4th floor). I guessed wrong—I thought the latter would be shorter because the first flight feels long, so we promised to work out together during the week.
After a refreshing workout, my friend treated me to dinner at Souvla (2505 3rd St, San Francisco, CA 94107), a Greek restaurant nearby. The food was super clean and delicious. I definitely want to try more items from the menu next time. We also had some great conversations about research on the way there. Talking to someone going through a similar situation but who has thought deeply about it always gives me a new perspective. I’m really thankful for that.
I went to bed pretty quickly after getting home. To be honest, I haven’t been feeling 100%. I’ve had a runny nose and some sneezing, though I don’t feel particularly sick or tired—just a weird cold-like vibe. Hopefully it’s nothing serious.
Lab Work
Chemistry
- SJ-1-34 purification
Thursday, May 8
167.5 lbs (Day 132, starting from 162.6 lbs on Dec 28) | 🏃🏻 Rest (3/6) | ★★★★
Outside of Work
I decided to skip the gym today since I wasn’t feeling 100%. I could tell my body needed a break. In the past, I used to push myself no matter what, but looking back, it always backfired and led to longer downtimes. These days, I’ve learned to let go of that kind of pressure, and honestly, it feels much healthier.
Today was already the final session of my second minicourse. Thankfully, the presentation isn’t tomorrow but next Monday, so I’ll have the weekend to prepare more thoroughly. That’s a relief. Lab work was a bit intense today, but I also managed to finish installing Boltz-1 successfully. I’m now thinking about adapting AlphaFold3’s source code to extract MSA and templates directly—though, funnily enough, I just realized I could’ve simply set inference = false all along… classic, haha.
After work, I did laundry, prepped my meals for the week, and spent a bit more time thinking through the computational side of things before going to bed. Like I’ve mentioned before, when I’m just doing wet lab work, it’s easier to mentally clock out after hours. But with computation, it’s always “just one more thing” before I stop… I really need to work on setting clearer boundaries.
Lab Work
Chemistry
- SJ-1-35 rxn, purification
- SJ-1-36 rxn, purification, freeze-dry
Friday, May 9
167.6 lbs (Day 133, starting from 162.6 lbs on Dec 28) | 🏃🏻 Done (4/6) | ★★★★☆
Outside of Work
I started the day strong with a refreshing morning workout, followed by my favorite RIPS class. After lunch, I ran (probably) my final reaction, though you never know, depending on how the bio results turn out, I might have to make a few more🫠 Thankfully, I also managed to complete the purification smoothly.
In the early afternoon, we had a farewell gathering for a postdoc from my previous rotation lab, who’s heading off to join the faculty at Harvard in Biological Chemistry and Molecular Pharmacology. I had been working with him on a side project until recently, and he was incredibly helpful throughout. I really hope everything goes well for him there.
The PI gave him a commemorative plaque featuring the chemical structure of a key compound he synthesized—though I didn’t get a close look, I have to admit, I was very jealous🤣 It made me think: I hope I can also accomplish something meaningful and memorable during my PhD and finish it strong.
Lab Work
Chemistry
- SJ-1-37 rxn, purification, freeze-dry
Saturday, May 10
166.6 lbs (Day 134, starting from 162.6 lbs on Dec 28) | 🏃🏻 Done (5/6) | ★★★☆
Nothing special happened today. I enjoyed my weekend morning ritual🙂 peaceful rooftop swimming, followed by a bit of weight training. After coming back home, I focused on preparing for my Monday presentation.
To be honest, I’m still not entirely sure what kind of presentation format the professor expects. There were definitely good aspects of the course, but also areas where things could’ve been improved. It suddenly struck me that even when there’s a course survey, most students probably don’t write detailed feedback like an essay. At best, they might leave a quick comment I guess. So real improvements might not always follow. It made me wonder: what kind of incentives could be offered to encourage students to give honest, thoughtful feedback? I feel like that’s something PIs should seriously consider if they want to improve their courses in a meaningful way.
As usual, I also spent some time wrestling with AI and computation stuff. There are moments when I seriously think a lot of coding tasks could be mostly replaced before I even finish my PhD. With all this talk about “vibe coding” and next-gen tools, it might sound like hype, but in terms of efficiency and practicality, it’s honestly not bad. I just want to make sure I stay on the wave, leveraging these evolving tools while understanding the foundations well enough to keep up.
