End of Second Rotation
Table of Contents
Sunday, March 16
166.0 lbs (Day 79, starting from 162.6 lbs on Dec 28) | 🏃🏻 Done (5/6) | ★★★★
After working out, I spent the whole day preparing my presentation. I recently learned a powerful software called Prism (Comprehensive Analysis and Powerful Statistics, Simplified) and have been using it a lot. It feels amazing. I always used Excel before, and using this software is like discovering a whole new world👍 I also worked hard to learn Chai-1 so that I can run it on my school’s computation cluster. I’m testing out various structure predictions.
Monday, March 17
166.0 lbs (Day 80, starting from 162.6 lbs on Dec 28) | 🏃🏻 Rest (0/6) | ★★★★
Outside of Work
Today, I took a Reaction Mechanism final exam. The problems were harder than I expected, but since it was open-book, I managed to write down all my answers. I’m not sure how the results will turn out, but TAs said that if my overall score (including quizzes and problem sets) is an A, then no corrections will be needed, so I’m hopeful! Although the workload was heavier than I expected, I liked how the course let me see organic chemistry from different angles, and the parts on peptide chemistry and bioorthogonal chemistry were especially helpful.
I spent the whole day working on my exit talk presentation and nearly finished it. I even prepared a rough script. Suddenly, my mentor offered to look over it, so I did a quick practice presentation. I still have two days left before the final talk, so I need more practice!
Lab Work
It was a relief that the LC-MS finally came back! I immediately took the overnight labeling samples that had been stored at -20°C, thawed them, and ran the measurements. The measurement finished around 9 PM. The protein looked very good, and even though the signal was weak, one of the compounds I synthesized did label the protein🥳😭 I don’t have much time left before my presentation, but I want to be sure if my protein is unstable at room temperature, so I plan to repeat the room temperature labeling experiment tomorrow.
Tuesday, March 18
165.7 lbs (Day 81, starting from 162.6 lbs on Dec 28) | 🏃🏻 Missed (0/6) | ★★★★
Outside of Work
Today, I skipped my workout again (I promise to go tomorrow) and also missed the Journal Club. I focused on experiments and preparing my presentation. Even though I worked hard and felt nervous, I’ve looked at my slides so much that even with my limited English, I can speak well enough. So, I’m not too worried!
Lab Work
I shared some promising results I got yesterday with my mentor. I then ran a labeling experiment at room temperature, but after 2 hours, no labeling was observed. I figured that could happen, so I left it overnight(When I checked the next day, there was still no labeling. The professor explained that this can occur with reversible inhibitors at my exit talk). Interestingly, I also found that when we treated positive control(iodoacetamide), not only did the cysteine we introduced get labeled, but another native cysteine did too (with lower reactivity!). I organized the data and updated my presentation. Since tomorrow is the final day, I took photos of everything I’ve made so far and organized them well for the handover.
Wednesday, March 19
165.6 lbs (Day 82, starting from 162.6 lbs on Dec 28) | 🏃🏻 Done (1/6) | ★★★★★
Finally, the day of the presentation arrived. I went for a workout to clear my head, and the sky was literally on fire, so I took some photos and videos. I wondered if it was a good sign🙂 After one last check of my experimental data, I quickly made some more slides, skipped lunch, and started my presentation right away. It lasted a bit longer than I expected (over 1 hour and 10 minutes), but the mood was very good and I think it ended very well. I felt such happiness, almost to the point of tears, knowing I had given it my all.
After the presentation, we all went to a get-together, had some beers, and talked a lot with the lab members. They are really kind and supportive people. Thanks to them, I learned a lot and enjoyed my rotation. I left around 8 PM, went home, caught up on some overdue 핑계고, and finally had a long, peaceful sleep with all my tension gone. This day will be remembered as a very happy one for a long time.
Thursday, March 20
164.9 lbs (Day 83, starting from 162.6 lbs on Dec 28) | 🏃🏻 Done (2/6) | ★★★★☆
I overslept, enjoyed a good workout, and then went to the lab. I organized all the optimized protocols, raw data, processed data, and findings from my experiments, and sent everything along with a future plan to my mentor. Also, last night I emailed my professor my exit talk presentation file with a thank-you message. This afternoon, he contacted me to meet, so I joined the meeting.
The meeting went extremely well because we discovered hints for a new project while reviewing my presentation. Although it’s too early to be sure, my professor suggested using the computation tactic from the structure prediction model I used to predict the structure of other proteins with a covalent ligand. I even got the chance to lead that project. During the meeting, he immediately emailed some related graduate students in our lab, including my mentor, about the idea.
It’s an amazing opportunity, but with a journal club presentation next week and the spring quarter starting the week after, I’m going to have to study a lot. Haha. Still, I feel really good.
After the meeting, I took a short break at home before heading out for dinner with two Korean PhD friends and one postdoc. We went to Dumpling Home(298 Gough St, San Francisco, CA 94102), a place a friend had introduced to me before that turned out to be incredibly delicious. I highly recommend it. One friend, who goes there regularly, ordered the recommended dishes, and they were amazing. the Numb & Spicy Pork Xia Long Bao and Juicy Pork Bao are a must-order!
After enjoying a tasty dinner, we took a self-driving taxi, WAYMO, back home. It was my first time riding in one, and it was very comfortable. I think it is perfect for when you want to chat with friends. The driving was smooth, and the car was a Jaguar, so the ride quality was good(better than a random Uber ride). Although sometimes the service might freeze, you can call the support center in real-time, so that’s not a big problem. The price isn’t too high either, but since my friend called it, I don’t know the exact cost.
Once I got home, I spent some time reading a paper the professor shared with me today. I thought deeply about the direction of my research and developed some hypotheses before finally falling asleep.
Friday, March 21
164.4 lbs (Day 84, starting from 162.6 lbs on Dec 28) | 🏃🏻 Done (3/6) | ★★★★
After carefully reading the paper and the email I received yesterday and studying for a while, I organized my thoughts and sent a reply about the project. I think research related to computational work has advantages and disadvantages. It can work endlessly without any space limits. But because of my personality, once I get into the flow, I keep going non-stop, which isn’t always good haha…I even forget to eat. After going to the gym, I read the paper carefully to prepare for the following Tuesday’s presentation. I have a meeting with my coach professor next Monday to review it, so things are tight!
Saturday, March 22
164.7 lbs (Day 85, starting from 162.6 lbs on Dec 28) | 🏃🏻 Done (4/6) | ★★★★☆
Today, I slept in comfortably, worked out, and then spent time preparing for my presentation. I also continued studying the project we discussed with my professor. I want to try another structure prediction model, but I’m having a bit of trouble integrating it with the cluster because the method is different.
In the evening, to celebrate the end of the term, I had dinner with a few friends from my cohort at a nearby restaurant called Wooly Pig (2295 3rd St, San Francisco, CA 94107). I ordered their signature dish, Wooly Pig (Shanghai style braised caramel pork belly, arugula, pickled red onions served on a toasted brioche bun), and had a side of tom yum soup (it was the soup of the day). It was delicious! The smoked flavor of the pork belly and the well-balanced other ingredients were amazing. Since the restaurant is so close, I might visit often.
After dinner, I spent even more time at my computer, working on my presentation and studying.
