Coming events cast their shadows before them I: Something is not the same

 

To complete my new job application, I had to obtain an apostille for my Ph.D. degree. For those who, like me, may not be familiar with what an apostille entails, allow me to clarify. An apostille is essentially a seal affixed to a document, and it serves as a verification by the receiving country that the document is indeed legally valid and has been issued by an accredited authority.  In my case, I pursued my undergraduate studies in Colombia, and later, my Master's and Ph.D. in Brazil. In fact, when I first arrived in Brazil, they required me to have my undergraduate diploma apostilled as proof that I had obtained my physics degree from a recognized institution, namely my university. Now, my situation has reversed as I have returned to Brazil to have my postgraduate diplomas apostilled, thereby rendering them valid for international use.

The black hole in the box

Taking as an excuse the legalization of my doctoral degree, I decided to revisit Brazil once more, embarking on a 12-day journey to the land of samba. As I am currently in the process of saving money before commencing my new job (which is another story worth sharing in the future), I reached out to friends and asked if I could stay with them. Fortunately all of them were very happy and dispossed to having me!

Reconnecting with my friends during this trip was an absolute delight, filled with wonderful memories and, of course, an abundance of delicious Brazilian cuisine. However, amid the joyous reunions and culinary indulgence, some thoughts that had been lingering since I concluded my job in Poland began to intensify. The reason being, I find myself no longer certain about whether I wish to pursue an academic career anymore. In fact, I have several friends which decided to left an academic life and moving to work for a company or for a bank, and during my trip I had the chance of experience a bit of how their lives changed since they left academia.

My flight landed at Guarulhos International Airport in the metropolitan area of São Paulo. Although my Ph.D. studies were in Campinas, a city approximately 128 km from São Paulo, I had a compelling reason to visit São Paulo city. A dear friend of mine is currently a postdoctoral researcher at the Universidade Estadual de São Paulo (commonly known as USP). She shares my background as a computational material scientist, and interestingly, her supervisor was a former student of my Ph.D. advisor. Therefore, visiting her and her research group became an essential part of my trip.

As soon as I arrived at my friend's place, she greeted me with a classic Brazilian breakfast: a Tapioca filled with eggs and cheese, along with a steaming cup of coffee. Our conversation covered a wide range of topics, from our days as Ph.D. students to our current roles as Postdoctoral researchers, where we're now guiding the next generation of Master's and Ph.D. students through their academic journeys. During our chat, we had a good laugh about something interesting. We've started to understand our advisors better, sort of like how you see your parents in a new light as you grow up. Amidst all the stories we shared over breakfast, my friend couldn't resist bringing up a particular memory. It's a tale she loves telling, and I'll share it with you here, this is the story about how we became friends:

René: Hey Jessica, word on the street is you're the newest addition to our research group. Funny, Alex didn't breathe a word about it. Anyway, let me introduce myself. I'm René, currently wrestling with the intricacies of the glass transition and atomistic simulations based on Molecular Dynamics. It's a pleasure to have you here. By the way, where are you from?

Jessica: Hi René, nice to meet you too. Yes, the rumors are true; I've just landed here, and we're going to be in the same group. I guess Alex didn't mention it because I won't be working directly with him. My Ph.D. advisor will be Maurice. Like everyone else in our group, I also work with simulations, but on a smaller scale than what you do. I specialize in electronic-level simulations using Ab initio computations. Delighted to make your acquaintance! I'm Brazilian, though not from São Paulo. I hail from the southern part of Brazil, specifically Paraná. What about you? Where are you from?

R: Ahhh, so we're in the same group, but with different advisors and research topics. That explains it! Maurice is amazing; I've been living in his Dutch shadow! I put in a lot of effort to speak Portuguese like a native, and even though I've reached a pretty decent level, everyone here always says, "You speak Portuguese very well, but it's not quite like Maurice. He sounds just like a real native." As for your Ab initio research, it sounds intriguing. You delve more into quantum mechanics, don't you? I've never tried it or even read about it. But what do you mean when you say "a smaller scale" than me? It's still atomistic simulation, isn't it? By the way, I'm from Colombia, a small city in the north called Barranquilla. It's famous because Shakira was born there.

J: Oh, wow, the city of Shakira! That's cool; your hips don't lie, do they? And I can't believe Maurice isn't Brazilian; he has absolutely no foreign accent when he speaks. I'm shocked! But don't feel bad; your Portuguese is seriously impressive. If you hadn't mentioned it, I'd have thought you were Brazilian. There are just some vowels you open a bit more than natives, but those are minor details. Now, regarding your question about scales in atomistic and electronic calculations, I think it might be easier to explain with a drawing.

Alright, let's kick things off with this central image, which resembles a planetary version of an atom. You've got the nucleus sitting right in the middle, with electrons whizzing around it. We know that atoms don't actually look like a solar system, but this model helps us get a better grasp of what's going on. In your case, with atomistic simulations, you consider the entire atom as a hard sphere, almost like the electrons don't exist, and the atoms can move around like ping pong balls with a diameter of about 10^-10 meters. Think of it like that orange ball you see in the lower left part of the figure. Now, in my line of work, we dive deeper into the behavior of the electrons. It's a very, very simplified way of describing it, but if you were to imagine electrons as ping pong balls too, they'd be roughly 10,000 times smaller than the nucleus. So, you can see, we're operating on a completely different scale here.

R: That’s a clean explanation, thanks a lot Jessica, but what are you exactly computing now? I mean do you also work with glasses?

J: Ah, you're curious about my research topic, I assume? Well, I haven't come across too many studies of structural glasses conducted by first principles. Typically, researchers in this field lean towards molecular dynamics or Monte Carlo simulations, but that's not really my cup of tea. Currently, my focus is on crystals, particularly those involved in concrete formation. Right now, I'm comparing experimental crystalline structures with my simulations. The catch is that these first principles calculations take weeks to complete, even for very small systems. To give you an idea, I'm dealing with just 120 atoms at the moment.

R: Oh my Lord! And here I am grumbling about my molecular dynamic simulations with 20,000 atoms taking hours to complete. I promise not to complain anymore. Well, okay, I might still complain from time to time – spoiler alert: I've never stopped complaining about my simulations taking forever. In fact, as I write this post, I'm grumbling because my current simulation is taking a full two days to finish. Some things never change –. But now, you've piqued my curiosity. Alex has tasked me with finding the crystalline structure of some alloy. Do you think you might be able to locate some experimental results I can use in my simulation?

J: Oh, come on, René! If you're running simulations and you get results in less than a week, you're on the privileged side, my friend. Anyway, let me take a look in the database I have here. I might be able to find the experimental unit cell for this alloy... Aha, found it! It seems this alloy has three different crystalline structures. What kind of chimera are you studying, René, for God's sake?

R: I know, the alloy I'm delving into is quite the remarkable metallic glass. This implies it's rather challenging to coax a crystal out of it. Hence, I believe that's precisely why there are three different versions—each one possibly obtained through a distinct method. Could you kindly send me these structures? I'll need to scale them up and run some molecular dynamics simulations on them.

J: Of course, René! I'm sending those unit cell structures right away. However, I'd like to offer a word of advice. These unit cells contain a maximum of 8 atoms, and I understand you typically require at least 10,000 for your calculations. But keep in mind that the parameters in experimental unit cells can vary slightly in comparison to real-world experiments. So, before you dive into a large-scale simulation, I recommend conducting extended simulations with these smaller ones I'm providing. This way, you can ensure everything runs smoothly. And if you need any assistance or run into issues, please don't hesitate to reach out. I'm here to help!

Once Jessica sent me those samples, I headed straight to my computer and got to work on them. Now, I've mentioned this quirk of mine in a previous post, but I've got this stubborn streak when it comes to free will. My will always seems to be at odds with the advice my friends offer, and as expected, I didn't follow Jessica's advice this time around. I mean, come on, I'm the one who specializes in molecular dynamics, while she's concerned about the size because she works with ab initio methods, which can be considerably more resource-intensive. So, I decided to take her advice in my own way. Instead of creating a sample with 10,000 atoms, I'll settle for 1,000 in my molecular dynamics simulations. This should be roughly equivalent to working with 8 atoms in ab initio calculations – That's me speaking confidently, despite my lack of knowledge –.

After two days when my simulation finish I got this:

As time passes, some of my atoms mysteriously vanish, and eventually, a black hole emerges in the center, devouring the remaining atoms. If it weren't for my scientific background, I might playfully attribute this to Brazilian witchcraft. There was a colleague in the room with whom I had a strained relationship, and I would humorously (seriously) speculate that he had cast a spell to make my atoms disappear. Even today, when things go awry, I half-jokingly think it's some form of Greek witchery. But it's probably best not to delve further into this topic; perhaps I'll save it for another post. 

"Because I couldn't just tell Alex that my Brazilian office mate jinxed me, resulting in my atoms turning into a black hole, I had to approach Jessica and inquire whether she had a more 'reasonable' (though I was still convinced it was Brazilian witchcraft) and scientifically grounded explanation for why my simulation turned into a black hole."

R: Jessica, I could really use your assistance. There's something amiss in my simulation—my atoms are vanishing, and eventually, a black hole emerges, consuming the remaining atoms. I have a fairly good hunch about what might be causing this, but I'm curious if you've encountered a similar issue before.

J: Let me take a look, René, at what's precisely happening in your simulation. — I'd like to mention that as soon as she saw the black hole in the middle, she recognized the problem — René, did you equilibrate the sample I sent you before scaling it up? Please don't answer, it was a rhetorical question; of course, you didn't. This is a pressure issue. As I mentioned earlier, the parameters in experiments often differ from those used in simulations. With the values you're currently employing, your sample is essentially generating a negative pressure. In a physical experiment, this would mean that the sample's pressure is lower than its surroundings. However, in simulations at the atomic level, achieving negative pressure involves creating a 'hole' in the simulation box to reduce the pressure inside. You're encountering this 'black hole' in your simulation because you didn't determine the correct parameters in the smaller sample and instead applied the experimental values to the larger one. While it's true that experimental and simulation values shouldn't vary significantly, when you scale up, the errors from the original 8 atoms are magnified across your 1,000 atoms. However, you mentioned having a hypothesis about why this is happening. Was this your line of reasoning?

R: Oops, I may not have followed your advice to the letter, but my line of thinking was somewhat along these lines. I had a theory, although it involved a human conspiracy. However, your explanation seems to align much more with the actual problem. Thank you so much, Jessica!

J: No problem, René, but you should exercise a bit more caution with advice. Typically, in the realm of science, we seek help when we've run out of ideas. So, if someone suggests a course of action, it's generally a good idea to follow it before resorting to 'improvisation." — She playfully made air quotes when she said 'improvisation.' — By the way, Jean, my boyfriend, is on his way to join me for lunch. Would you like to come along?

We went out for lunch together that day with Jessica and Jean, and from then on, we became very close friends. Among other things, both of them taught me about Brazilian culture—music, TV shows, pop references, and more. Even now, when I meet Brazilian people, they often remark, 'It's incredible how immersed you are in Brazilian culture. It's not just the language; you know the TV shows, the slang, the food, the songs—it's like talking to a native.' I can only attribute this to Jessica and her famous line, 'Porra René, how is it possible you don't know that? Let me enlighten you on this.'

As we grew closer, I shared with her my theory about why the black hole appeared in my simulation box. Even now, she laughs about it and shares the story with everyone, recounting how we became friends because of a black hole in a box. Of course, we laugh about this story during our breakfasts before heading to her new research group at USP. 

It is not as enjoyable as it once was

Since we had spent almost the entire morning engrossed in conversations about our academic journeys, we arrived right on time for Jessica's meeting. While she was in the meeting, I decided to spend my time exploring the physics department. During this stroll, I passed by the post-graduate student association, the cafeteria, the library, and even the bookstore that I used to be eager to visit in the past. However, for some reason, I didn't experience the usual excitement of being in the university—of doing physics, envisioning my future as a professor, contemplating which courses I'd teach and how I'd teach them. It was as if I had suddenly found myself in an unfamiliar environment, as if I were trying to force myself into a place where I no longer felt like I belonged. I though this will be because the USP isn’t my alma mater or a place where I’ve got my knowledge. However, I experienced the same sense of detachment when I was in Colombia and visited the university where I completed my undergraduate studies. There's something within me that has changed, or perhaps has already changed, and I can't quite put my finger on it. I still vividly remember how thrilled I used to be, spending my days from Sunday to Sunday, from 7 a.m. to 11 p.m., at the university. I cherished the joy of giving lessons and teaching physics, and even after I finished my undergraduate studies, I continued offering free physics classes to those who were interested. I always resisted the idea of merely preparing students for exams, teaching them how to solve problems solely for the purpose of passing a test, without imparting a deeper understanding. There was only one instance when I felt compelled to do so, when I needed extra money to apply for my Canadian visa. During that period, I felt utterly miserable, as if I were compromising the integrity of my profession as an educator. Once Jessica's meeting concluded, I joined her, holding onto the hope that once I arrived at the University of Campinas, where I pursued my Ph.D., all my feelings of unease would dissipate, and I would once more be captivated by the academic ambiance.

I spent four days at Jessica's house, during which we had the opportunity to explore the key attractions of São Paulo and meet members of her research group.  It became evident that newcomers in the group were grappling with familiar academic challenges. The government's scholarship cuts had left many postgraduate students exceeding their expected study duration, forcing them to seek jobs as their financial support dwindled. Some appeared disheartened by academic life and contemplated alternative career paths, or even pondered leaving academia prematurely, without completing their degrees. Once again, I found myself wrestling with a sense of discomfort in this academic environment, plagued by the feeling that I didn't quite belong. However, the big day arrived and I was on the road to Campinas city to visit my university. If I've lost any motivation to continue in academia, Unicamp, as we usually call the university, will surely reignite that spark.

The Cabrera effect

I arrived at the Campinas transport terminal in the afternoon, and even though I could have taken a taxi to the university, I decided to relive my student days by taking the bus I used to ride when I lived in Campinas. In our fast-paced world where everything undergoes continuous change, the bus route to the university had altered its usual stop near the physics department, leaving me 1.5 km away from my destination. Now, it's worth mentioning that Jessica had suggested I take an Uber from the bus terminal due to the post-COVID chaos, but, of course, my stubborn free will won the day.

After a 30-minute walk to the physics department, which, all things considered, wasn't too bad since it gave me the opportunity to traverse almost the entire university on foot (thanks to that bus dropping me so far away), I found myself flooded with a wave of fond memories. Every building I passed triggered a multitude of recollections – both the highs and lows of my university days. I reminisced about my initial insecurities of living alone and far from my family, my fears of not being able to complete my master's degree, and the friendships I forged along the way. Every corner of this university held a memory for me. Despite doing my undergraduate studies in Colombia, I truly became a physicist in Brazil, and Unicamp is undeniably my alma mater, or at least that's what I felt as I strolled towards the physics department.

I completed my Ph.D. online in May 2020 due to the COVID-19 situation. During that time, I was in Quebec, where I had undertaken a research internship, and I had already secured a postdoctoral position in Poland. So, I had left Brazil in December 2019 with the expectation of returning in August 2020 to defend my doctoral degree. However, the universe had other plans, and it wasn't until 2023 that I found myself back at the Unicamp physics department. When I entered the office I used to occupy, it felt as though time had stood still. Everything on my desk was exactly as I had remembered it – my books, my magnets, my post-it notes, my CDs – as if I had simply left the day before and had returned to continue working.

I only had three days in Campinas because I had already planned to visit a friend I made in Canada who lived in another state. She had already booked my tickets to go there, so I needed to make the most of my time during these three days. First things first, I visited the university's academic directory to request my Ph.D. diploma. Later, I rushed to the notary's office to get the apostille, as this was the primary reason for my trip to Brazil. It was amusing that this entire process took no more than two hours, and I had traveled all the way from Colombia for it (and to visit my friends). Since I still had some time before my friend could pick me up – she was working and would meet me later in the evening – I sent a message to my Ph.D. advisor to see if he was available for a quick chat. Fortunately, he responded promptly, and I quickly made my way to his office to reunite after four years.

R: Hi Alex, how's everything? It's been a while since we last saw each other in person. Have you lost weight? You look a bit thinner.

Alex: Fala René, everything's going well here, and how about you? In fact, we haven't seen each other since you decided to learn this dead language and move to Quebec. And it's true, I haven't completely recovered from getting COVID. It was a tough time, but I don't know if I told you, I knew exactly when I got this. I knew who infected me. – My Ph.D. advisor was like a father figure to me in Brazil. He always supported me, taught me proper Portuguese, recommended books to read, and, most importantly, he instilled in me a love for research. Before I met him, my goal was to quickly finish my postgraduate studies and find a university that would hire me to teach. However, he showed me the importance of being a researcher, the respect for the profession, and most importantly, how I could become a better professor through research. On the flip side, my Ph.D. advisor has a very sensitive heart, and he'll never forget if someone had a bad attitude towards him or if a student didn't approach him before discussing something with other professors, or didn’t appear in the classroom when he was the professor in charge. So, I can only imagine that the unfortunate soul who infected him with COVID will be in his bad books for the rest of his life! –

R: Is this true professor? did you get COVID? oh my God, and no you never told me about who infected you. It was a professor here? 

A: Yeah, I got Covid, but it wasn't a professor from here; it was someone from USP. My wife and I were at a celebration dinner for one of my colleagues, and this person was sitting at the same table as us. I told my wife, "This guy is coughing too much, it's not normal. We should change tables." But in the end, she said I was being paranoid. Guess what? The next day, we both felt sick, and my wife received a message from a colleague saying that the person in question had been diagnosed with Covid. She recommended that everyone get tested. Of course, I was furious, so I went to the pharmacy to get tested, and, as expected, we were both infected.

R: Ah professor, I’m really sorry you and your wife experienced this bad situation, but I’m happy you’re both good now.

A: I am not good René, I haven’t recovered completely, everything for this guy who didn’t have responsibility to stay at home, and me too, I should stayed at home, tough times René, tough times. But enough about that. How has your return to Unicamp been? Any new plans in the works? And how's your research coming along?

R: Alright, Professor, I hope you recover soon. As for me, things are going well. I'm currently in the process of changing jobs, moving from Poland to France. I'll be working at an aerospace center with responsibilities split between Lyon and Paris. Returning to Unicamp has been quite nostalgic, but it feels a bit different this time, as if something is missing. On a side note, I noticed that almost all the cafeterias on campus are closed. The only one I saw open was the one in the Biology department. It gives the university a somewhat deserted feel, I must say.

A: Oh, indeed, you're absolutely right. It seems like another post-COVID effect. By the way, do you remember Professor Cabrera, the one who taught you statistical mechanics? I recall you mentioning that you preferred taking that course with him instead of with me. – as I mentioned before, my Ph.D. advisor never forgets anything he considers an affront. Anyway, I ended up taking two courses with him later, but he always remembered that I didn't take statistical mechanics with him. He used to tease me about it, saying those were tough times –. Well, the thing is, Professor Cabrera has retired now, but during his last years here, he would arrive late in the afternoon, teach his course, and then leave without interacting with anyone. It's interesting that post-COVID, there's what I like to call a "Cabrerization" happening at the university. People come to campus quietly, stay for just an hour or two, and then head out. For instance, I only come here when I have a class to teach, and afterward, I simply leave. And that's pretty much what most people seem to do these days.

R: Hahahahah, a "Cabrerization" of the university! You'll never change, Professor. Hahahahaha, that was indeed quite good. Oh, I almost forgot, I need to pick up my documents from the notary. Would it be alright if we discuss my research tomorrow? I have some questions I'd like to ask you. I'm currently working on a manuscript about ultra-stable glasses, and I'd really appreciate your input.

A: Of course, René, it would be a pleasure. Tomorrow, I have to participate in a qualification exam, but what do you think about meeting for lunch around 11:30, and afterward, we can chat about glasses?

R: Sounds good, Professor. See you tomorrow!

A: By the way, René, where will you stay here in Campinas? Did you rent an Airbnb or a hotel?

R: Ah, no, Professor. Today, I'll be at Mariana's house. Do you remember her? She was your student in condensed matter physics. She'll pick me up later tonight.

A: Is she the one who was a student of Monica from the Department of Applied Physics? She's a fifth column, and I think she doesn't like me too much.

R: I don't think she has any strong feelings about you, Professor. It's interesting; I haven't heard the expression "fifth column" in a while. By the way, I got interested in the Spanish Civil War thanks to you. Anyway, have a good afternoon, Professor.

A fifth column

A fifth column… I haven’t heard that expression since 2018 when Alex said to me for the first time…