Chemical Biology in the Bay Area Day
Table of Contents
Sunday, April 27
168.0 lbs (Day 121, starting from 162.6 lbs on Dec 28) | 🏃🏻 Missed (5/6) | ★★★★
The other day, some fellow PhD friends visited a newly opened Korean market in Daly City called Jagalchi (63 Serramonte Center, Daly City, CA 94015), and they said it was pretty good. So I decided to check it out with a friend afterward. To sum it up in one sentence, it felt like they brought over a Korean department store food hall. I got really excited seeing what looked like authentic Korean dishes for the first time in a while.
We tried a bunch of different items, but…😢 nothing quite hits like the real thing in Korea. Ironically, I never really craved Korean food that much back home, but now that I’m here, I find myself wanting it more than ever. I’m not yet sure if I’ll be able to visit Korea this summer, but if I do, I’m absolutely going to eat everything I’ve been missing until I’m sick of it.
Actually, Jagalchi is a famous fish market in Korea, but all we ended up eating was bunsik (snack food)! Still, I’ve heard from friends and other Koreans who’ve visited that the seafood here is actually pretty good, so next time I’ll definitely give it a try.
After that, we walked around the connected mall for a bit and had fun browsing random shops. Once I got home, I took a quick nap, but I couldn’t sleep too deeply because I still had some data analysis left for my manuscript. I’m not sure if it’s the final round of analysis, but I wrapped up as much as I could and made major edits to the draft. I’ve been feeling under the weather since Friday, so the plan is to submit it tomorrow and finally get some solid rest.
Monday, April 28
167.2 lbs (Day 122, starting from 162.6 lbs on Dec 28) | 🏃🏻 Rest (0/6) | ★★★★☆
Outside of Work
I went to bed really late last night, and I was still feeling a bit under the weather, so I skipped my workout and took some medicine. The weather was nice though (the first photo is the view from my lab!), and even though I was sniffling, I was in a decent mood. After class, I wrapped up my draft and headed to the Hub in the evening to work on my blog. Later, I had dinner with my friend at Four Kings 四大天王 (710 Commercial St, San Francisco, CA 94108).
Everything we ordered was delicious, but the seasoning was quite strong for me, probably meant to be paired with alcohol, so I’m not sure I’d go back again🧐 Still, the atmosphere was nice, the menu was cute, and I’m a bit bummed we didn’t try their signature dishes. The pork cutlet was good too, but it made me miss the ones I used to have at pork cutlet places in Korea🥲
Lab Work
Chemistry
- SJ-1-23 rxn, purification
- SJ-1-24 rxn
Tuesday, April 29
165.1 lbs (Day 123, starting from 162.6 lbs on Dec 28) | 🏃🏻 Done (1/6) | ★★★★
Outside of Work
I had things to do early in the lab this morning, so I headed there quickly and then went to the gym. Recently, I noticed I’ve lost a bit of weight again, so I decided to increase my carb intake slightly. I usually stick to the same meals (overnight oats for breakfast and turkey with marinara pasta for lunch), so it’s easy to track and adjust my calories based on my weight trend. Sometimes that just means adding 10g more pasta at lunch or an extra tablespoon of peanut butter in the morning.
Today was quite busy with a new type of chemical reaction I needed to run, so I worked straight through without taking a break. After work, some of my cohort were playing basketball at the gym, but unfortunately, when I got there, the court was reserved, so I couldn’t join🥲 Hopefully next time I’ll get in a game. It’s NBA playoff season now, and I’ve been enjoying short game highlights. Maybe that’s what’s making me crave actual games even more. After getting home, I did some meal prep and fell asleep pretty quickly.
Lab Work
Chemistry
- SJ-1-23 NMR check
- SJ-1-24 purification, NMR check
- SJ-1-25 rxn, work-up
- SJ-1-26 rxn, work-up
- I had never performed Fmoc deprotection before, so I followed the most common reaction conditions: using a secondary amine in DMF.
- However, the desired product (a free amine) turned out to be water-soluble, even though the molecule contains bulky, aromatic groups. As a result, I ended up evaporating the entire reaction mixture for purification. Since DMF can interfere with separation on a silica gel column, I’m considering using a reverse-phase C18 column instead. DMF usually elutes quickly (within about 2 column volumes) under weak solvent conditions, especially at the start of a reverse-phase gradient where the mobile phase is mostly water.
- Next time, I might try using DCM and simply allow a longer reaction time. Although some literature suggests that DMF provides faster reaction rates, I believe that extending the reaction time could compensate for this difference. Plus, DCM is much easier to evaporate, allowing for direct loading onto a column, which would make the process faster and more reliable overall.
Wednesday, April 30
165.6 lbs (Day 124, starting from 162.6 lbs on Dec 28) | 🏃🏻 Done (2/6) | ★★★★
Outside of Work
I managed to succeed in going to the gym in the morning! Today was also a busy day because I had two meetings. One was a group meeting, and the other was a qualifying exam practice for a graduate student from the lab I previously rotated in. The group meeting was really great. My mentor presented the full story of his research project from the past two years. He’s worked hard (you can tell by the data he’s collected) and did a fantastic job organizing the story, which is going to be a solid foundation for the manuscript.
I also appreciated the comments from the PI. He pointed out some weaker aspects of the data and suggested future directions that could strengthen the core message of the potential paper. Most importantly, he emphasized the motivation and significance of the research, “how it addresses a widespread limitation in the current field.” He said no one’s interested in just replicating existing work; what matters is having an advantage. Once that goal is defined (how the research overcomes the limitation), we have to stay laser-focused on that strategy throughout the paper. That made a lot of sense to me. I’m already looking forward to the next group meeting!
After lunch, I attended the qual practice. I can’t imagine I’ll be doing the same thing around this time next year. Two hours, no slides, only a whiteboard, and tons of deep, unexpected questions. It made me even more determined to choose a thesis project I can fully dedicate myself to, since I’ll need to invest so much time into it to pass the qual and develop the idea.
After the meetings, I wrapped up some remaining tasks, did some house chores, wrote a blog post I had been putting off, and went to bed soon after. The day went by unbelievably fast.
Lab Work
Chemistry
- SJ-1-25 purification
- SJ-1-26 purification
Thursday, May 1
165.6 lbs (Day 125, starting from 162.6 lbs on Dec 28) | 🏃🏻 Done (3/6) | ★★★★☆
Outside of Work
Typical day—gym and class🙂 Minicourse is so short that I only have two classes left already. I’ll need to start preparing my presentation soon, which will be about the analysis of my mass spectrometry data.
Today was also the first time I went to a bar with my current lab members, and it was great! We were celebrating a successful annual thesis committee meeting of a graduate student in the lab, as well as my mentor’s well-received group meeting presentation yesterday.
It was nice to talk in a more casual setting. I had the chance to ask them more directly about the lab culture, the PI, and the pros and cons of the environment. Through those conversations, I learned a lot about the lab, the PIs, and their research perspectives, which was super helpful. I definitely need to reflect on all of this more seriously when I get the time. After the outing, I took a late nap, got some work done, and went to bed again.
Lab Work
Chemistry
- SJ-1-25 LC-MS, NMR
- SJ-1-26 LC-MS, NMR
- SJ-1-27 rxn, work-up
- SJ-1-28 rxn, purification
Friday, May 2
166.7 lbs (Day 126, starting from 162.6 lbs on Dec 28) | 🏃🏻 Done (4/6) | ★★★☆
Outside of Work
Today, I went to the lab first, ran a few reactions, and then hit the gym. After my favorite RIPS class, I focused on experiments. I ended up leaving the lab close to 8 PM for the first time in a while. It didn’t feel like I did all that much, but maybe it’s because I did three rounds of purification.
At home, I did some meal prep and cleaning. Since there’s a chemical biology conference at Berkeley starting early tomorrow morning, I pretty much went straight to bed.
Lab Work
Chemistry
- SJ-1-27 purification
- SJ-1-29 rxn, work-up, purification
- SJ-1-30 rxn, work-up, purification
- Similar to Fmoc deprotection, I had never done Alloc deprotection before either. The Alloc group doesn’t give a strong UV signal on TLC, so I had initially wanted to avoid using it, especially since it can lead to side products under LiBH4 reduction conditions in the scaffold I am using.
- However, the deprotection itself turned out to be much cleaner than Fmoc, even though I had used DMF for the Fmoc reaction. Surprisingly, I was able to purify the product on silica without any issues, despite the TLC for the Alloc deprotection showing multiple spots.
- That said, I still think using Fmoc (but a different solvent for the deprotection) would be better. Throughout the synthesis, it’s easier to monitor the reaction by UV, which also makes purification by automated flash chromatography more efficient. Also, there’s no side product during reduction.
Saturday, May 3
167.0 lbs (Day 127, starting from 162.6 lbs on Dec 28) | 🏃🏻 Missed (4/6) | ★★★★★
Today, I went to the 2025 Chemical Biology in the Bay Area Day conference at Berkeley with some of my cohort. This event alternates between Berkeley and UCSF each year. It usually includes talks by professors, but this time it featured only student presentations and a poster session. I thought it was mandatory for first-year CCB students… but turns out it wasn’t haha… Anyway, it was a great experience to hear about a wide range of research areas in chemical biology.
The most memorable talk for me was about a method called LC-seq, a sequencing-based separation strategy designed for DNA-encoded libraries (DELs). This approach enables massively parallel, single-molecule evaluation of both synthetic fidelity and lipophilicity (an important property related to membrane permeability) for each individual compound in a DEL. In the presentation, they applied LC-seq to a 120,000-member peptide library and analyzed synthetic efficiency across all reaction steps, revealing interesting structure–reactivity relationships. The really cool part was that the on-DNA lipophilicity values (measured directly while DNA is still attached) strongly correlated with off-DNA lipophilicity and passive permeability. By separating molecules based on their interaction with the LC column (I am not sure now but I think they used a quaternary amine on the DNA tag to isolate the peptide portion), each cyclic peptide produced a distinct chromatographic pattern. This method makes it possible to directly assess the quality and drug-likeness of DEL compounds at an unprecedented scale, which could have a big impact on future drug discovery efforts. Pretty cool.
We had lunch at a wide-open grassy area overlooking the library, then attended the poster session and had a great time. Afterward, we stopped by Yogurt Park (2433 Durant Ave A, Berkeley, CA 94704) for ice cream, on the recommendation of a friend who did her undergrad at Berkeley. I went with mint and chocolate yogurt with Oreo topping, which is hard to go wrong👍 Under the beautiful sunshine, we made our way back to SF.
At home, I did my usual meal prep. I’ve been doing it every three days lately since I switched my protein from ground beef to chicken thighs, which come in three-day portions per pack. I also did a serious deep clean, scrubbing the floors until they were gleaming. It felt great. I went to bed early, and thanks to all the sun I got today, no insomnia at all lately.
