A “running account” of a year
Winter
At the beginning of the year, I was working for a collaborative project. Still soaking in the lazy atmosphere of the New Year holiday, I was suddenly splashed by a bucket of cold water: I found a very stupid mistake of mine. The cause of this “accident” was that I set the PBC box size too carelessly during the initial stage of the simulation. Two systems that should have been strictly compared actually had completely different volumes. This made the results look “surprisingly beautiful”, and as expected, any result that is too beautiful deserves suspicion.
After the panic, I had to calm down, write emails to apologize, and explain the whole story. Then I fell into a long period of low mood. I found that no matter how I tuned the simulation parameters or even modified the model itself, I couldn’t get results that matched the experiments. So I was forced to start from the most basic system to explore possible reasons for failure. Throughout January, I spent almost every day thinking about a problem that seems very obvious now: How can a particle that only provides “attraction” suppress the formation of condensates by scaffold molecules? Until one day, I decided to add a “repulsion site” to the original model, and everything became smooth. Of course, there should be two beads! One for attraction, one for repulsion. This also fully proves that valency is not “the higher the better.”
So in February, I even came up with a statistical model that looks a bit like “real physics” to determine the specific simulation parameters. I am glad my collaborators all accepted this new model. More large-scale simulations confirmed my guess: the single-bead model always acts like glue; only when we introduce the new repulsive bead does the model gain special regulatory ability.
Spring
In late February, I learned that my KAKENHI grant application passed smoothly. In early April, I received an unexpected award notice. These made the “perceived temperature” of the whole spring rise a lot. However, the cherry blossom season did not arrive early.
Our GENESIS website was suddenly attacked by crazy spam advertisements, so we received a “rectification request” from the management department. I thought: why not just migrate it completely to a more modern static page framework? Unfortunately or fortunately, this task miraculously fell on my head. I thought not many people knew I was maintaining my personal website, but this “perfectly matched” job actually found me by itself.
In early May, I started the overall design, including file structure, technical framework, color style, etc. By late May, we had a “not too ugly” shell. Then I mobilized the whole group to check various pages. From this group mobilization, I also happened to see the different personalities of various people.
In mid-June, it was already so hot that I couldn’t walk from Himeji Station to Arcrea Himeji under the sun without sweating. In December of the previous year, I was here as a “weird 20%” organizer for another conference, which left me with not-so-good memories. However, Himeji in this early summer might be one of the few “highlight stages” of my life. On June 20, I won the Young Scientist Award from the Protein Science Society of Japan. I probably broke two records: the oldest age, and the first Chinese winner.
At the end of June, our GENESIS website went online officially at mdgenesis.org . I was responsible for almost all the development work.
Summer
The high temperature in the air penetrated my body and suppressed all my passion for work. It seems no inspiration can spark in the dry heat. I just mechanically continued the work route from the beginning of the year.
Several projects seemed to fall into a “tug-of-war”. I repeatedly did many comparison tests, the simulation trajectories were extended again and again, and the data analysis repeated the same actions. My collaborators, for some reason, also almost stopped moving.
In summer, I started planning a busy autumn. From September, I entered a state of “running around.”
In mid-September, under thunder and rain, I attended the last annual report meeting of a large research project. The participants were all old acquaintances, and the research results were not very “eye-catching”. However, I gained many beautiful memories in the hotel where the meeting was held. The theme of the hotel was “rice fields”. Yes, some designer really dared to use this element as the theme for a two-story medium-sized hotel. My room was in a “not bad” corner, almost no neighbors, and outside was the rice field. At night, I could sit on the terrace, listening to frogs and watching stars – if it wasn’t raining. But rain is the best tool to put out all kinds of “delusions.” Turn off all light sources except the desk lamp, play one piece of chamber music from some unknown orchestra, and then I could happily hit the keyboard. No need to worry about affecting anyone; everyone was isolated in other worlds by the sound of rain. When the three-day meeting ended, I had already finished the draft of all the computational parts for a new paper.
Autumn
I even forgot how many meetings I attended this autumn. I only felt that while shuttling between various transportation tools, the E-book reader is a great tool to kill time and avoid awkward eye contact.
The Biophysics Annual Meeting is almost a social gathering for old friends. This year there was also a 60th birthday party for my former boss, and I happened to see many “industry seniors” who are usually hard to sit with. Several of them, I met again more or less in other meetings in October and November. Maybe the volume of Japan is too small, making the probability of meeting at conferences far exceed the level necessary for information exchange.
The most boring meetings often have the most “scary” themes. I attended an exchange meeting that gathered dozens of Nobel Prize winners, and the content was listening to them tell “success stories”. Some illusions easily break when the “real body” is placed in front of you. The Nobel Prize in Physiology or Medicine seems to be a “circle”. Only when you build enough connections within the circle will you get (then you get) the chance to be nominated… This is the story I seemed to hear. These old men, it’s as if they just went to school, did work, won the prize, and then stopped all thinking, becoming super mediocre ordinary people, no longer seeing any sparks of wisdom. :P So, don’t attend this kind of meeting; it makes it too easy to feel hopeless about life.
Other Dimensions
Reading
Talking about reading, of course, I don’t dare to talk about any “serious” books. I almost didn’t finish a single book this year. During a business trip on the Shinkansen in March, I started reading “Tokugawa Ieyasu” by Syouhachi Yamaoka. By June, I started making jokes like “this book is as long as Ieyasu’s lifespan” to cover the embarrassment of my reading speed. I didn’t expect that by the end of the year, I only finished 6/7 of it.
The author should be a master of writing about love. The stories of Hirotada and Odoi, Ieyasu and Tsukiyama, Nobunaga and Nohime, Nagamasa and Oichi, Hideyoshi and Nene – all are vivid and touching. The unique female perspective in the book also makes one yearn for the rare “maternal generosity” and the mind that can embrace the whole world. It is a book worth reading again.
Gaming
In the middle of the year, I bought Sid Meier’s Civilization VII during a sale. The interface and operation feel better than the previous generation. However, in my heart, the soundtrack failed to surpass Civilization VI.
Before the release of Octopath Zero at the end of the year, I didn’t have time to finish the first generation. Probably, I have reached an age where I cannot get enough happiness from games.
Music
Every evening, I practice the fingerstyle of the song “Childhood Days” (少年时代). Finally, at the end of the year, when I must frequently toast my hands on the heater to prevent them from freezing, I linked the song together and played it to a level that is “barely listenable.”