Episode 7 - Aleksei Aksimentiev: Nanobiotechnology, the importance of mentoring, and engineering serendipity

In the seventh episode, Aleksei Aksimentiev and I delve into the intersection of physics, biology, and nanotechnology, exploring the innovative world of nanopores and biomolecular sequencing. Aleksei shares his journey from particle physics in Ukraine to leading-edge research in the US, and underscores how on the unpredictable path of scientific discovery, openness to new ideas can lead to groundbreaking advancements. Alongside, we discuss the pivotal role of mentorship in fostering scientific curiosity and the pursuit of ambitious goals, illustrating how a supportive mentor can be the key to unlocking potential and driving forward the frontier of biophysics.

Transcript

0:00

Welcome to the phase space invaders podcast, where we explore the future of computational biology and biophysics by interviewing researchers working on exciting transformative ideas. Today, I'm talking to Aleksei Aksimentiev, a group leader at University of Illinois Urbana Champaign, whose work is focused on exploring the interface of physics, biology, and nanotechnology. The most prominent line of his research is the study of nanopores. both protein and solid state in which the sequence of a biomolecule can be inferred from experimentally measurable ion currents during translocation. However, his group has also been pioneering the use of molecular simulations in the study of large scale nucleic acid assemblies from DNA origami to genome packaging in a viral capsid. So Alexei brings up many great background stories of how these devices came to life, how most of his projects were born out of his openness to explore new scientific territories, and how he ended up in Klaus Schulten's lab in Illinois in the first place. He makes a great case for embracing uncertainty and ambitious goals. But then we also discussed the role of mentoring in this process. And how a great mentor can imbue us with a sense of wonder and direction that will put us on a path to great scientific contributions. As a side note, inspired by our off record chat about Alexei's family back in Ukraine, that's just my reminder to reach out to your colleagues who have family and personal lives in Ukraine. Not only in Ukraine, but zones of war and human right abuses in general. I know this is sensitive and complex topics, so I won't share any generally applicable words of wisdom, but support, listening, understanding, and giving space are often the least we can do. With that being said, hope you liked today's conversation. Let's go.

Milosz: 2:14

Aleksei Aksimentiev, welcome to the podcast.

Track 1: 2:17

It's my pleasure.

Milosz: 2:19

So Aleksei, I got to know your scientific profile as part of the extended Schulten family at Urbana Champaign, a place that has been a powerhouse for computational biophysics for, you know, at least three decades now. you find your happy spot closer to nanobiotechnology or the practical application of biological structures. to problems like nanopore sequencing or DNA packaging. only recently I realized you initially moved from studying particle physics in Kyiv to the PhD in material science lab of Robert Hołyst in Warsaw. And do you see your research path as a natural consequence of those early choices of this early background? Or was there some serendipity involved?

Track 1: 3:02

Oh yeah, that's a great, uh, great question, actually, to start. I always like to tell the story. So yeah, I grew up in, in Ukraine I, I was always interested in how things, you know, what things are made of. also my parents were scientists, I went into first chemistry. And I mean, when I was in sixth grade, I thought, well, if I know how, Elements, are arranging themselves into compounds. I don't know something about, the world and, uh, but then I, I, I got to read a college textbook, uh, I just happened to have it and then the preface was about particles the particles like electrons and protons. And, uh, and then I realized I have to go to physics because that was my, uh, interest. So I entered, uh, Ivan Franco, uh, national University in Ukraine. Uh, which is in Lviv, and there I, I, I got my master's degree with specialty in particle physics, and that was in 96. So the Soviet Union already collapsed and we had an exceptionally, exceptionally strong class. Like from the whole, you know. 200 people, they selected out 10 and put them in one class in, in theory physics. So, of course, I wanted to do science, right, so I wanted to go, and do a PhD. And looking back at my scientific path, I think the best thing that happened to me, I didn't get into a grad school in Ukraine., I was probably at the pivotal moment because, uh, well, they had only spots. Yeah. And there were like eight of us or wanted to do it. Yeah. And then, uh, somehow, uh, there was this other person who used to go to Poland for work and he said, Hey, well, there's this opportunity, maybe you go do a PhD in Warsaw. Well, okay. Amen. All right and I was not involved in the communication with my future Ph. D. advisor, but they thought I really wanted to do something particle physics like. But the lab where I went was soft matter physics. So somehow they saw that, well, okay, so here's a project for you. Let's do field theory for polymers. You know, that's where you have this, uh, one loop approximations, cumulant expansions. Before Mathematica, it was super messy and complicated. But that's how I ended up with a topic for my PhD, which was polymers. Purely theoretical, lots of integrals and stuff. Yeah, that was total luck, yeah. Absolutely, I mean, what was maybe not luck is my decision to be open, like where to go. So I said, well great, so let's just see what Poland is like. It also helps that I knew Polish already back then. I've never spoken a word of Polish, but I knew it because back in Soviet Union we watched Polish TV it's near the border, yeah.

mi-osz_1_03-28-2024_150920: 6:01

That's interesting. Yeah.

Track 1: 6:03

yeah,

mi-osz_1_03-28-2024_150920: 6:03

thought

Track 1: 6:04

and, uh, so everything people could say on TV, I understood perfectly. Yeah. And after that, it was completely,

mi-osz_1_03-28-2024_150920: 6:10

I

Track 1: 6:11

also another random thing that happened. I was quick with my PhD, which I attribute to my, uh, advisor, Robert Hollis, so he was extremely, good at, realizing, someone's ambition So, so I unexpectedly graduated in two and a half years. And, uh, before I was considering applying for a postdoc position, another, uh, event happened. So, so it happened that a person from Mitsui chemicals was visiting Warsaw and and somehow we start talking and then it turns out that they, So happen have a postdoc position in my field of expertise, which is field theory for polymers in a chemical company in Japan, right? That's like coincidence. I don't know. Later on, I learned that there was a reason for it. But anyway, and so I actually never applied for my first postdoc. It's just, it found me

mi-osz_1_03-28-2024_150920: 7:09

see

Track 1: 7:10

so, so again, again, total coincidence, but again, I was open to learning new culture. It was interesting to go to Japan and see what it was like. What I guess was different was that it was in a company, Not in a university, so I didn't know what it would be. And it was very educational and, uh, it gave me also perspective on how things work in industry. because in my experience, industry is industry everywhere you go. So it's not just Japanese right, so I, Yeah.

mi-osz_1_03-28-2024_150920: 7:39

of talk of going back and forth between academia and industry.

Track 1: 7:44

Yeah.

mi-osz_1_03-28-2024_150920: 7:45

Always good to hear examples of successful transfers back and forth, that

Track 1: 7:50

Yeah. Successful, successful transfer. It's interesting. Uh, yeah, I think it's successful. I mean, in my first postdoc I was doing Simulation I was my first simulation work. Actually, we looked at phase separation and polymer mixtures, which is an interesting subject in soft matter physics critical phenomena and so on It was interesting, great stuff, so I love it. But, uh, it was actually Robert, my, my PhD advisor, who convinced me, not convinced me, he ignited my interest in biology. He told me, you know, Alec, uh, biology is the future. There's so many interesting things there, and he was, inspirational, So so I was convinced, okay, let's do biology. The problem is I didn't even know the difference between like proteins and DNA. Nevertheless, uh, nevertheless, I googled biophysics. And this is a true story. I googled biophysics. Klaus Schulten's lab was the first hit. 2001. 2001. It was just, uh, When, uh, well, it was end of, end of 2000 and that was, Google was very fresh on one of, one of the first, but, but, but Klaus's website was so incredible, powerful because when I joined here as a postdoc. I had my, of course, sites, you know, my entry. And if I were to Google my first name, which is a fairly common name, I would be top five hits, you know. He, just had this really big cloud in, in the Google space. But, but, but anyway, but, but that's a true story. I Googled biophysics and, uh, ended up in Irvine. I never heard of it before.

mi-osz_1_03-28-2024_150920: 9:25

That's cool. That's definitely serendipity. Yeah. this

Track 1: 9:29

Well, I would say there was a serendipity and choices, right? I knew I didn't want to do, I mean, face separation is interesting, and now there is, you know, renewed interest with its application to biological condensates. So, it is an interesting field. I just didn't feel I want to do it for the rest of my life and when, uh, you know, when you're going from one postdoc to another and you have a reasonable, uh, resume, that's your opportunity to change the field, which I took and, and I never regretted that I did.

mi-osz_1_03-28-2024_150920: 10:06

I think we very often fall in love with particle physics, right? Whatever takes us there. then we almost universally realize we're not going to be professional particle physicist. I think I had as a teenager, perhaps I went through the same phase at some point and you are much more serious in that approach, of course, but,

Track 1: 10:23

but you know, it's also, it's also my, as I, grew, uh, became an adult my perception of what is interesting to me changed as well my decision to switch to, well, biology, biophysics was driven by the same question. I was still interested in what it is that makes things around us the way they are. It's just I was no longer interested in abstract, you know, atoms. I was interested in, uh, in living things.

mi-osz_1_03-28-2024_150920: 10:53

That's a good point. So what about current field of research, which is nanobiotechnology?

Track 1: 11:00

Yeah, I mean, I would, I would say it's, uh, it's not just like nano biotechnology. We are fairly open to, to everything that has a biomolecular component. So we do classical biophysics problem as well. viruses, organelles, and so on,

mi-osz_1_03-28-2024_150920: 11:16

Mm

Track 1: 11:16

But, uh, I guess my lab specialty is modeling the interface between biological and man made systems very broadly I would say it holds a lot of potential for future, like, real life applications because biomolecular modeling, Typical questions are, how does enzyme A work? And, and so on. Sometimes it's a, it's a collection of enzyme. Now with a new computer system, you can do a larger system and so on. You can ask questions of, uh higher biological relevance, right? But still, we're still kind of far from actually saying, Oh, and the cell will die or in the cell will live, you know? So there's still a little bit of disconnect between. The molecular scale and what actually happens at the cell scale. And that is, of course, something that we want to bridge over the next, I don't know, 10, 20 years. But in the field of this bio nanotechnology or nanobiotechnology, the scale is confined So you are looking at the right scale. Which is the scale of individual molecules, maybe collection of molecules, and the scale of nanoscale devices that are built. So with, uh instruments and technology that we have, computational technology, we can model the relevant system, so to say, to scale and the results that you get, usually can be, well, usually may be very too strong one, but can be compared to experiment in some cases one to one. And, uh, it's also easier to make predictions that can be tested and, and vice versa. Um, you can use, simulations to interpret results of experiments.

mi-osz_1_03-28-2024_150920: 12:55

right, so perhaps more limited by your own creativity.

Track 1: 13:00

Yeah. I,

mi-osz_1_03-28-2024_150920: 13:01

the complexity of the system as you would

Track 1: 13:03

I should say since, since this is, this is kind of an open ended conversation, I must say that my path to that was also a little bit interesting. Okay, so I came to Claude Schulten's lab and I was really, oh my god, I was so happy. Finally, my first project was working on FOF1 ATP synthase. You know, the enzyme that makes ATP in our body and I said, that's an attribute to me being a complete newbie. I didn't realize how difficult the project was. I was like, oh! Yeah, of course. Yeah, let's do it. And somewhere in the, in the month nine, I realized, uh, we don't have a structure for the FO part. And what we were doing is a model and so on. Yeah. Well, anyway, so it was probably one of the most difficult projects that I've done as a postdoc. And, but don't get me wrong. I loved it. But, uh, okay, I got one publication out of it in two years, and that was really difficult. I'm proud of it, but it was, it was super difficult. Uh,

mi-osz_1_03-28-2024_150920: 14:12

and we're still, we're still working on the F1FO

Track 1: 14:15

it is, it's, it's very difficult. Well, now at least there are structures, right? Now at least there are structures, right? And, and before it was model, and I didn't realize that. Because I was a newbie, that's the difference between model and structure is how much people will believe, will believe what happens after, right? Well, anyway so Klaus's lab was in Beckman Institute, which is, uh, an place. So you have people doing, uh, psychology, uh, brain scans, uh, material science, like autonomous vehicle, things. And on the same floor, there was a person who was, former Bell Slab, uh, member. Uh, so he moved here. So he was into like extreme nanotechnology. So his name was Greg Temp. So he, he has influenced my trajectory tremendously. It's again, maybe a serendipity or not, but he was super energetic, organized this. weekly or by weekly seminars where he would invite people from campus and they would discuss crazy projects, like making a tiny device out of Silicon to put in bloodstream you know, that would, that he would power up with, uh, with radio waves and, uh, one of the questions was, okay, so let's say we make it. So what is going to do, right? And the idea was, well, we're going to use it. To sense things. And that's when this nano port sequencing came about. And the idea was, oh, okay, so we'll drill a hole through, through a gate of transistors. That was his, his spill and we'll sense whatever there is about, cells and so on. I was really excited by, by, by his vision. And I really like to work on the project. And so it happened, Klaus just got a grant on that and, uh, and I said, I want to do it. I want to do it. Let me do it. And I did it. So, uh, yeah, it was cool. I was really driven by it. Uh, it was interesting. No one has done anything like that, uh, before. Uh, you know, I have to adapt, uh, biomolecular force fields to. So we can nitride and, We learn a lot, you know, since then, since we did this first simulation. And I was in a way fortunate because of the environment in which I was doing it. So we had, developers of NAMD and VMD, you know, next door because we didn't know if it would ever work, you know, no one like simulated infinite crystal of silicon nitride in NAMD and, uh, and it just worked You know, there were a few things that, that, uh, Jim Phillips, NAMD developer, implemented to, to make it happen later on. We also ended up developing this, uh, uh, electrostatic analysis for VMD. it was really helpful to have access to developers, um, on site. But, I guess the programs were well written, so most of the time it just worked.

mi-osz_1_03-28-2024_150920: 17:09

And now it's something that exists out there, right? I mean, the nanopore sequencing, uh,

Track 1: 17:14

Yeah, Nanopore sequencing. So,

mi-osz_1_03-28-2024_150920: 17:17

at the, was it something that you had in mind at the time, or?

Track 1: 17:20

so Nanopore sequencing, of course, now is a legend in a sense so one can look back to a moment in time when, uh, Dave Dimmer and, Dave Brenton, they were driving, Along Highway 1 or something like that. And Dave Deamer had this idea, you know, well, you have a DNA going through nanopore and you read the sequence by measuring current. So that's a documented fact. So you can actually trace back this to 19, 87., The first, published work was, uh, done by John Kasyanovich, who is a pioneer in the field. So he actually showed that the nanopore sequencing is possible by experimentally moving strand of DNA or RNA molecules through, a membrane channel called alpha hemolysin so the idea of nanopore sequencing is that one reads the sequence. let's say DNA by measuring ionic current that flows through a pore. If the dimensions of the pore are of the same size as the dimensions of the nucleotide, you could expect to see differences in the ionic current as the DNA is passing through it. So that was basically the idea whether or not it would work back then, it wasn't clear, but John Kasyanovich experiment shows that one can actually do experiments and the DNA goes through it and you can actually tell homopolymers apart. So that was 96 and, uh, that kind of jumpstarted the field. Although were other works in the area that predated that like from, uh, Sergei Bezrukov, where they sense, molecular events using nanopores basically. It's single molecule sensing, but it was not sequencing. So, that was the idea. now. Would it work or not? That's a good question. I, when I heard of it, I was also, I was very excited. I, I had no doubt that it would work, honestly, because I didn't see, maybe because I work with atoms all the time, I didn't see a reason why it would not work, you know. But that's also maybe a bias of a theorist, because as an experimentalist, and now, now that I know a lot about experiment, I can also see many reasons why it would not work, you know. But, but, but the key.

mi-osz_1_03-28-2024_150920: 19:33

ask experimentalists, why shouldn't this work? And they always

Track 1: 19:36

Yeah.

mi-osz_1_03-28-2024_150920: 19:36

reasons.

Track 1: 19:38

No, but, but the key was actually having a, having a stable pore. You know, this is something that doesn't come to mind as a, as a simulator, but, uh, in reality, all of those pores are gate. They open and close stochastically, and that really doesn't help sequence DNA if it happens. And, kudos to John Kasyanovich and his, co workers that they did it because that was done without knowing the structure of the channel. Yeah. Do you realize the structure was, was shown later?

mi-osz_1_03-28-2024_150920: 20:04

is

Track 1: 20:05

Yeah. Yeah, so I, I had no doubt that it would work, but Greg Timp convinced me that, you know, all those biological pores, it's rubbish. The key, we're going to do it with a solid state pores, right? because we know how to put billion transistors on a chip, and so we can have billions nanopores on a chip and do sequencing. So in a way, this is really transformative and a cool idea, uh, and, and I was sold on it. By the way, it's still not done, but, are issues when you put semiconductors into water. So we know how to do really tiny lithography with synthetic materials in vacuum once you put it in salty water, you know, things grow, dissolve, and there are all these dielectric capacitance that you don't think of used to working with air and so on. So there are many reasons it won't work, but I think it can be done in the long term.

mi-osz_1_03-28-2024_150920: 21:03

That's why we need physicists still, yeah

Track 1: 21:05

yeah That was, um, I really liked that project.

mi-osz_1_03-28-2024_150920: 21:08

Do you think you're at the stage where you can say technological progress with simulations, with ideas these days, or is it still kind of more in the explanatory or data fitting phase? All

Track 1: 21:26

in this field of bio nano, uh, I, we are not data fitting, for sure. With the current state of molecular dynamics, uh, a lot, we can get the currents reliably for structures that we know their structure, right? Of course, if we don't know their structures and we don't know their chemical composition, then, uh, then it's an order of magnitude kind of result. But if it's, um, truly a biological channel, then we We should be able to get the, the current right and if we don't, that usually means our interpretation of experiment is wrong But that's, that's kind of what I, what I learned. It could be that the protein is misfolded or something else. Is there, we are at that stage that we are expect to get the number right. And if we don't, then probably something wrong with the underlying assumption.

mi-osz_1_03-28-2024_150920: 22:14

Okay.

Track 1: 22:15

to answer your question directly, you know, if, we can drive the technology development Yeah, absolutely. So, coming back to this nanopore sequencing, so the problem with conventional nanopore sequencing was that the electric field was used to do two things. To pull the DNA through and to move ions through the pore so, the faster you pull the DNA, the more current you get, so you get the higher signal, but the less time the DNA spends in the pore, so you actually get a shorter read. So that doesn't help. and the other way around, if you, uh, apply lower bias, A, you can capture DNA, but even if you capture, then your ionic current is low. So, around 2008, Jens Gundlach, and his lab, they came up with a new pore which shape was just perfect for DNA sequencing. It has a very narrow constriction. And then Mark Atkinson, uh, from UC Santa Cruz, so he was developing enzymes to independently, control the speed of transport So you combine those two and you have nanopore sequencing working, right? So, so that, that kind of, Worked and, uh, was realized, uh, experimentally back in 2012. But the point I was, I was trying to make is that before this enzyme, you know, was invented to do, we also tried to engineer a nanopore surface so that it would bind DNA stronger, so it would kind of naturally slow it down, right and I was at that point was thinking to myself, but also to my students and postdoc saying, you know, if you like, say you go to sleep and you wake up with a sequence you know, that does it well, then you're a billionaire in a way. I mean, seriously, because it's very transformative. The time it goes from, Oh, this is a sequence that will work to, to the points that you actually implemented in practice, probably a few months. And then of course you write, uh, disclosures and then all of those things. It was a very short, uh, kind of timeframe from idea to real life impact, which I liked a lot. Uh up with this, we didn't design, but, uh, We are working, actually, it's one of the areas of research for us, to design custom pores for detection of custom modifications on DNA and RNA, and of course, protein sequencing nanopore sequencing is done now. It was commercialized by Oxford Nanopore Technologies I guess, disclosure, so I'm working with them. So I guess I have to say it. But yeah, they, they have a device and you can buy and it works. Yeah.

mi-osz_1_03-28-2024_150920: 24:58

Yeah, I know that there's a lot of work going into detection of modifications, right? Because this is such a hard thing to study with all the other setups, the other experimental techniques that a direct detection is the only way to get good quantification and good results placement

Track 1: 25:14

Yeah. Well, non prosequencing is, is kind of the only method that actually reads. It's the native DNA because usually you do some kind of amplification to use the product of it. Uh, well mass spec, I mean, if you can do single molecule mass spec, that would be another way to do it, but we are very far from that happening. But for the nanopore, the next frontier is protein sequencing. There's a lot of interest in protein sequencing. especially detection of all of the PTMs. So there, the number of modifications is, is, well, it's not astronomical, but it's huge. And, uh, you want to do it at a single molecule level and there's simply no technology to do it. With nanopore sequencing of DNA, you by the time DNA started, we already had technology We always tricked nature to do it for us, like feeding it with, uh, fluorophores that it cannot digest and so on. Uh, and nanopore sequencing was, uh, We would read it by physical means. but because they were already, existing technology, it was up to the market to determine which technology would actually work. And that is something that is outside the realm of science, as you understand

mi-osz_1_03-28-2024_150920: 26:26

Yeah,

Track 1: 26:27

yeah.

mi-osz_1_03-28-2024_150920: 26:27

non scientific forces at play.

Track 1: 26:30

But with protein sequencing, there aren't really that many. Well, right now there are a few companies that have alternative methods for protein sequencing, but it's not, it's nowhere near being done, so we'll see what will happen

mi-osz_1_03-28-2024_150920: 26:46

I can see the appeal of having a technique that will give you the right statistics of each modification, right? When you can combine with pull down assays, you can select for things that are bound to DNA or bound to a specific fraction of DNA..

Track 1: 27:00

yeah. The other area where we active our so called DNA nanotechnology. So that's where we use DNA as a building material. And I'll go back to Ned Seaman and his invention of DNA nanotechnology the way we know it. Paul Rosenmoon inventing DNA origami and so on. So, That was also a field that I was looking at since the beginning. It is cool. It has this huge, cool appeal which is why it ends up at the covers of Science and Nature but there wasn't anything for us to do there. You know, that's also, if someone thinks you know, when do you enter the field? Well, there should be a reason to enter the field, and our reason was, uh my friend and collaborator, Erlich Kaiser, so he wanted to make nanopores out of DNA. So that, that's actually how we got into it. So nanopores out of DNA, so the appeal is that you can make them of any size, and it's DNA, you have good control, and, uh, so Sanjeev Jung Yoo was a postdoc in my lab And he is incredible. And I said, well, why don't we do this? And he's like, well, yeah, but maybe first we do origami. I'm like, okay. 24 hours later, okay, so here it's running, it's like, what?

mi-osz_1_03-28-2024_150920: 28:20

It's great to have those people in the lab,

Track 1: 28:24

No, he's, he's incredible. And, uh, yeah, so that's how we did this first, uh, all atom simulation of DNA origami, just because, it was there. So in a way it was like climbing Mount Everest of course, we learned something about it, but our drive was to say that we can do it. But once we had the technology to do all atom simulations of systems, of course we start exploring making predictions. So that is also one of the areas where I can pinpoint two instances where we discovered something by looking at all atom MD simulations So, for example, we were interested in those DNA nanopores, right? So DNA nanopores, you make, uh, it's like a membrane channel, but made of DNA. Of course, DNA is charged, so it doesn't want to go into the membrane. So to make it go into the membrane, you decorate DNA with something hydrophobic. So there's like a ring of, hydrophobic moieties that wants to insert into the bilayer. And if conditions are right. Then the insertion happens and the DNA goes in. So we were looking at, uh, at that just to see how much current actually is leaking through the walls, because DNA is not super compact So you would assume that some of the current would flow along the walls of the DNA. And indeed, you know, we did see that well, okay so that was nice. We had this result and the, we're writing up two papers with Kaiser's lab. And then I was at the meeting, uh, and tell her, right. So, my name is Aksim Intiev, and the person who organizes the meeting, he had this very ingenious way of organizing talks, just alphabetically, as a person, there was only one person before me, his name was, I will mispronounce, but it was A. C. So, he was right before me, and he was talking about biological scramblases. So, scramblases are the enzymes that scramble lipid composition. Okay. I maybe have heard of them before. I mean, I've of course heard of flippates and floppates, but, uh, but those are active ones. But passive ones, like, like I was looking at his talk and I was like, uh huh. I think we've made a scramblers out of DNA origami because, you know, once you place it in, you, you fuse the two, uh, the two leaflets and, uh, and I wrote an email to, to my student who was then in the lab and said, well, can you actually see if lipids go from one side to the other Of course, they did. But then, but then what happened, we, um, So we of course sent this result to Urlik Kaiser. And his student actually spent two years. measuring it experimentally. This is not an easy experiment, especially if you're not doing this for a living. No, no, that's, uh, that was a learning process for him and, uh, for the lab because we, I mean, then once they know how to do it, they did it multiple times, but so I really, uh, grateful to him and, and, uh, and Kaiser lab. So they invested so much time into actually showing that this happens experimentally. And, uh, I think we had a nice paper out of it was, Multiple, uh, possibilities, potentially for using it for all kind of medical applications.

mi-osz_1_03-28-2024_150920: 31:39

It's good to be on the lookout for alternative usages of something that doesn't work as intended.

Track 1: 31:45

No, but that's, I mean, this is an example where you actually see something in a simulation and you say you're making prediction

mi-osz_1_03-28-2024_150920: 31:51

okay. So, to switch gears, wanted to mention the topic of mentoring in academia. Yeah. Can you elaborate on that?

Track 1: 31:59

Right. So mentoring, of course, is essential and frequently underappreciated part of, uh, academic, life. as you go through ranks from, from, uh, from undergrad students to professor, you switch roles from being mentee to being a mentor. And, uh, through my, uh, own experience, I can attest that that probably was one of the most essential parts of, of my, uh, of my career path and, and, and my success. my undergrad, I probably can say that I didn't get much mentoring, yeah. It was. Kind of ad hoc, and that was also a style of Soviet education. You had courses and, and, and that's it, right? So you do well, fine, but everything changed when I, when I moved to Poland and, uh, and my PhD advisor, Robert Hollis, so he, he was a fantastic mentor. I wish, uh, you know, I could be like him. He had this, ability to ignite interest in people in their work. And, uh, just, work, but, kind of broader. You know, doing science, it's so fun, you know, and so on. But, it, it is a personality thing. You know, I, I don't think it's so easy to replicate. That's why some mentors are better than the others. But. To me, it was, it was essential. I got interested in actually pursuing a career. science because of him

mi-osz_1_03-28-2024_150920: 33:28

Yeah, I see. I have to say, I think the quality I appreciate in mentors and that's my personal thing. I don't know if it generalizes, but it's people who can say, you know, maybe we fail in a spectacular way, but it would be a lot of fun to do it and this kind of approach that, oh, yeah, it's a lot of work. You know, it doesn't always. work out but. It's a tremendous fun to try new things and break things.

Track 1: 33:54

Yeah,

mi-osz_1_03-28-2024_150920: 33:54

inspiring. I agree with that.

Track 1: 33:56

that's right and, uh, mentoring now is popular. I don't know how it is in Europe, but in the U. S. Mentoring is one of the things that grant agencies require you to have. And I think it's a good thing because very frequently nobody pays any attention to it. On the other hand, there is

mi-osz_1_03-28-2024_150920: 34:16

mode in academia.

Track 1: 34:17

Yeah, yeah. On the other hand, there is a tendency to institutionalize mentoring, and I see nothing wrong with it. Uh, I think it's, it's good to have seminars and talks manuals on how to mentor but of course there is a, there's a degree to which it can go. You know, at the end of the day, mentoring is, um, It's a psychology exercise between a mentor and a mentee. And, uh, and the success of it, of course, depends on both parties involved. But that's my personal take, okay? So, um, that's how I think about it. I learn a lot from my mentors about, you know, What actually going on, how, how the referee process works, right? Because mentors, you know, they've been on both sides multiple times, especially if you have a mentor who is also an editor of a journal. So, you know, it's even a third perspective. You know, this is something you're not going to read somewhere, And some things, of course, are set in confidence but that is insight into how the process work is incredible. Yeah. And, uh, if you are,, a student and serious about, successful career in academia, ask your mentor about it. It's, uh, it will really, really help you a lot. Yeah.

mi-osz_1_03-28-2024_150920: 35:35

I agree. I also agree it requires curiosity on the side of the student, to

Track 1: 35:40

Exactly.

mi-osz_1_03-28-2024_150920: 35:41

Oh, like, please

Track 1: 35:42

Exactly. Now,

mi-osz_1_03-28-2024_150920: 35:44

because they

Track 1: 35:45

it's

mi-osz_1_03-28-2024_150920: 35:45

boring

Track 1: 35:45

not

mi-osz_1_03-28-2024_150920: 35:45

death, but Uh,

Track 1: 35:48

not like that, you just, yeah, and it's, it's like one thing that I learned from, from Klaus Schulten, who, who was a great mentor as well, was, uh, so he always said, you know all this referees, and it goes to publication and, uh, and specifically, in particular grant applications, you know, it's psychology. I mean, of course, it has to be great science, and that's true, but that's given, right? There are so many great sciences, but at the end of the day, it's just psychological exercise, because you're convincing someone, and that someone is not a robot, it's a person.

mi-osz_1_03-28-2024_150920: 36:23

Yeah,

Track 1: 36:23

that's kind of insight, I don't know, if I would ever actually come up with myself, maybe, maybe later on, uh, but, knowing it, early on was really helpful.

mi-osz_1_03-28-2024_150920: 36:33

a good, very good, insight. Yeah.

Track 1: 36:35

yeah, but, uh, but, you know, mentorship, it goes both ways I don't think there are too many mentors who would refuse a meeting with a, with a mentee. You know, it's always, it's our job. You know, it's our job to give advice and, uh, and counsel people. the other hand, uh, we can, uh, can't chase students and enforce mentoring, you know, that's also not good

mi-osz_1_03-28-2024_150920: 36:58

the

Track 1: 36:58

to a degree.

mi-osz_1_03-28-2024_150920: 37:00

kind

Track 1: 37:00

It has to be, it has to, it goes both ways. And generally I think everyone, wants to see their students succeed, students postdoc succeed because as a success of students in postdocs, that's probably the biggest accomplishment for for a mentor

mi-osz_1_03-28-2024_150920: 37:17

yeah, that's what we eventually take pride in.

Track 1: 37:20

Yes, exactly.

mi-osz_1_03-28-2024_150920: 37:21

Okay, So, Aleksei Akhmetyev, thank you for the great conversation and sharing

Track 1: 37:27

Thanks so much.

37:28

Thanks so much. It was a lot of fun. Thank you for listening. See you in the next episode of Face Space Invaders.