My First Preprint📝

Sunday, September 21

159.2 lbs (from 165.4 lbs on Aug 24) | 🏃🏻 Done (7/6)

https://www.biorxiv.org/content/10.1101/2025.09.16.676163v1

Finally, my first bioRxiv preprint came out: Single-sequence deep learning delivers crystal-quality models of covalent K-Ras G12 hotspot complexes. I really appreciate Qinheng and Kevan for helping me grow a tiny idea into something that could help the scientific community. Hopefully, I will soon get results in my thesis project that I can be confident about. Stay consistent!💪

 Later, I wrote a blog post and did meal prep. I recently bought a Ninja Flip Toaster Oven and Air Fryer, and today was my first run with it. The results were awesome. No more stirring several pounds of chicken thighs for twenty minutes. Just cut into pieces, season, then use Air Roast for 20 minutes at 400°F. Total game changer. Meal prep became much easier. I am even considering buying a second tray so I can swap trays instead of washing between batches when I load chicken breasts. I highly recommend it, and it also saves a lot of counter space by flipping up when not in use. Why do the appliances keep multiplying?😂

After that I went for an indoor run and did a quick 5K. Running indoors feels harder than outdoors because I get distracted more easily. It is boring to stay in the same spot, maybe because it was my first time in a while running indoors. Unless there is heavy rain or bad weather, I do not think I will do it again😳

Monday, September 22

159.5 lbs (from 165.4 lbs on Aug 24) | 🏃🏻 Done (1/6)

With wonderful weather I had a refreshing Monday workout. I am glad my pace of losing weight is close to the goal I set at the start of the diet. I probably need one to two more months, but it hasn’t been hard because I am progressing at a slower, sustainable pace. I will share the results in a post once I reach the goal.

For the first time in a while I did some organic synthesis. It felt physically intense, probably because I’ve been doing only computational work lately. I cannot believe I did over 1,000 reactions during my master’s. Maybe that’s why my physical and mental health were not optimal then. I felt real gratitude today that I can pursue both directions when needed.

In the afternoon I had my third one on one meeting with Kevan, and it went well. It is awesome that he regularly makes time to check in; it really helps me organize what I have done since the last meeting. Keeping with that theme, I recently started posting a biweekly progress update in our shared folder, which my PIs really like. I truly think that in graduate school, consistency at a manageable pace is the best practice. After sending the meeting summary I went home, did a bit more work, and went to bed early.

Tuesday, September 23

159.7 lbs (from 165.4 lbs on Aug 24) | 🏃🏻 Done (2/6)

Nice back workout, then I spent most of the day on synthesis. It was my first time purifying a dye molecule. The column fractions were beautiful (each one bright and a different color), but the purification didn’t go well because the dye was poorly soluble and there were many side products. The paper I followed reported about a 20% yield, so it was not surprising that mine was similar or even lower. After a lot of troubleshooting, I managed to isolate the desired compound at a comparable yield, but it was mentally exhausting and time consuming 🥲

In the afternoon, there was a farewell party for a postdoc who had been here for nearly seven years. Congratulations to her on the new job. I am cheering her on. After work, I was so tired that I fell asleep right away.

Wednesday, September 24

159.4 lbs (from 165.4 lbs on Aug 24) | 🏃🏻 Done (3/6)

Brutal but satisfying leg workout, then a DeGrado lab group meeting. The speaker was my rotation mentor. He has great personality, deep expertise in synthesis (he earned his PhD in total synthesis), and computational enzyme design. He’s helped me a lot, and I really appreciate it. I was not doing synthesis today, so I focused on computational tasks in the lab. I realized that starting with the smallest pieces and gradually increasing complexity is the key to getting comfortable with new software. Once I am accustomed to the architecture (which takes time), I can pursue more complex, integrated workflows efficiently. I also tend to over-research before starting, which sometimes keeps me from getting a hands-on feel for how to use the tools. I need to be more prompt and a little less perfectionistic in my learning.

After a productive day, I went for a run at a slower pace, doing English conversational practice with ChatGPT Voice. It was much better than a few months ago. Definitely more responsive, natural, and human-like. To speak clearly, I had to slow down below my preferred pace, so I am deciding how often to do this while still improving my running and endurance.

Thursday, September 25

159.2 lbs (from 165.4 lbs on Aug 24) | 🏃🏻 Done (4/6)

Workout, just quickly set up an overnight reaction, then focused on computational work. I ate lunch with a graduate student in the DeGrado lab. He kindly suggested we meet up; he is also a joint student (but with a different lab) pursuing a direction that differs from both labs, so it was a great chance to share opinions about balancing two groups. Much appreciated. I focused on work in the afternoon, went for a run, and had a relaxing evening.

Friday, September 26

158.8 lbs (from 165.4 lbs on Aug 24) | 🏃🏻 Done (5/6)

Today was quite a busy day. The amide coupling reaction I set up yesterday (using a compound I recently synthesized as the starting material) did not proceed well. In hindsight, it was likely the low reactivity of the amine (a sulfonamide). Checking the SI again, they ran it at 60 °C overnight with about eight equivalents of coupling reagent. To make matters worse, someone had changed the flash column solvent line (not as the default), so I ended up purifying on the reversed-phase system without TFA; many peaks were severely broadened throughout the run😨

Even though the morning was unlucky, I took a RIPS class for the first time in a while (my favorite class so far😄), which quite recharged me. I also made some progress on my computational work, so I left work feeling a little happier. Since I ran yesterday and the day before, I decided to skip running, focus on work in the evening, and get some good rest.

Saturday, September 27

159.1 lbs (from 165.4 lbs on Aug 24) | 🏃🏻 Done (6/6)

Did a fresh morning yoga class. It was led by a different instructor, and it was decent, but I think the Sunday 9:00 a.m. class is tougher and gives me a more fulfilling session. I have already taken six classes and I am considering another class membership. Surprisingly, the price is relatively similar to, or even cheaper than, group classes in Korea.

After class I went to Bageletto (76 14th St, San Francisco, CA 94103) again, and had a salmon bagel served open style. It was really great. The only downside is the price😇

After getting back home I did some work. I have started to prefer computational work over wet lab work😉 It is so convenient to focus from anywhere. After work, I went to an old-school, 24-hour eatery (Pinecrest Diner, 401 Geary St, San Francisco, CA 94102). With generous portions, the omelette and onion rings were really good, but the other dishes were just so so…, and the hash browns were not good at all. It seemed like they had been sitting out after cooking for a while. Maybe next time I will just have a simple protein and egg combo. I love the diner vibe, but I still prefer Millbrae Pancake House, where I went with my cohort.