Ukrainian engineer worked on one of the first 3D images of the coronavirus — interview

The resident of Kryvyi Rih, Yuri Svyrydenko, used to work in the metallurgical industry. Now his scope of work is biotechnology and 3D visualization of medical processes and objects. He founded a company and moved to California. In winter 2020, his team participated in the development of one of the first detailed and scientifically proven 3D visualizations of the coronavirus SARS-CoV-2.

AIN.UA’s editor had a conversation with Yuri about the history of this visualization.

Could you tell me about your interest in biotechnologies?

The story of my love for biotechnology is pretty long. Ever since I was a child, I liked biology and microorganisms; I studied them through a microscope. My friend and I even had a competition — to find, describe, and depict microorganisms as much as possible.

I dreamed of becoming a surgeon. But it was too expensive to rent an apartment, so I went to the Kryvyi Rih National University to study “electro drives and automation of industrial systems and robots.” However, I still loved biology and started learning programming and bioinformatics.

During my last years at the university, I worked at the Kryvyi Rih Metallurgical Plant as the engineer for complex system setup and management system automation. I have worked at both blast furnaces and rolling mills.

How did you start with biotechnology visualizations?

Sure, I was missing biology all the time. I read news, books, and professional newspapers. I thought about medical electronics and drive systems; biomachines interested me (for example, flagella of bacteria that work like an electro engine). I started to visualize such things.

The scientifically proven visualization in biotechnology and medicine is quite useful. It shows you how all is done and how everything works. You can even zoom it in to separate molecules what is impossible for the naked eye. Scientists and everybody interested can learn complex molecular mechanisms using such a visualization, for example, how to synthesize ATP.

During 2001-2003, together with startuppers from Moscow, I developed a website about nanotechnologies, Nanonewsnet. We published news and preprints from foreign media there. At that time, we needed to make our own visualizations. We could not just take some pictures from foreign media and publish them on our website. That is why I started to learn 3D editors, especially 3D Studio Max, to create illustrations.

I recall how I earned my first money for the 3D visualizations: we wrote a big article about cryonics [Editor’s note: low-temperature freezing and storage of a human corpse]. We created illustrations for the article with 3D Studio Max, and they became viral. First, in the USA, then in Europe. Everybody was speaking about them. After that, we got emails with requests to use my pictures. There were published some postage stamps with our pics. You can find them even today if you enter “nanobot cell repair” on Google. Internet remembers:)

It was a breaking point for me: I sold my copyrights for those pictures for $1500 and understood that I could earn money now. I remember that I have purchased a new mountain bike.

How did you launch your biovisualization campaign?

Our nanotechnology news project slowed down, and we didn’t understand how to monetize it. I quit the project. But the website is working nowadays too. I began to develop engineering solutions for heating and water supply and kept working on visualization simultaneously. During this period, from 2005 until 2012, I collected a lot of experience in this field. I managed to draw not only pictures but also animations. Here is one of the videos that got great feedback among scientists — the animation of cancer metastasis mechanism:

Then I met my future business partner Andriy Koniukh. Together, we started building Nanobot Medical, a medical visualization company. We created videos for pharmaceutical companies (Pfizer, Novartis, Bayer, etc.), high schools, research labs, medical entities.

Examples of medical 3D visualizations made by the company:

About four years ago, I moved to San Diego, California. I live and work here now.

How did you join the coronavirus project?

Our other activity is video creation for startups. Many companies in Silicon Valley were founded by teachers, professors, or ex-students. Many of them could have brilliant ideas about technology, but they failed to present it right to an investor. The investor has 2 or 3 minutes to decide, and the startupper should convince him during that short time. And it is easier with a video than a presentation or a simple pitch.

So, in January 2020, we have learned about Turn Therapeutics from Y Combinator and met its team from Scripps Research, San Diego. The startup came to Y Combinator with an idea of a medicine that would stop coronavirus in early stages.

At the time, we knew almost nothing about SARS-CoV-2. We knew that it was spreading in China, and that’s it. The startup offered us to draw coronavirus and show how it affects the cells. They had some articles of Wuhan scientists, and we had visualization and crystallography capacity thanks to Scripps Research’s scientists. We decided to collect all the data, study how the coronavirus works, and show how it looks.

3D visualization of the coronavirus from Nanobot Medical, all photos in the article are provided by the speaker

Within just a few months, we created videos and pictures. We finished our work at the time when Trump declared a lockdown. The startup got a big discount from us because we had a lot of fun working on this project. There was a feeling that we did something significant and good for the whole world.

How did you create pictures and videos of the coronavirus?

After a month, we created pictures and structural visualization of the virus itself, and then we worked on a video during the following two months. We constantly checked the data and requested feedback from the scientists.

We have got a lot of data about virus microscopy from the startup and the Scripps Research team. And I believe the picture of the virus came out pretty truthful. For example, many authors draw coronavirus with symmetric spikes and smooth form, but it is not. In the fact, these “spikes” (spike proteins) often have an irregular structure. Their number can vary from 30 to 120.

The data about the virus surface was obtained with a scanning electron microscope. For that, we must extract a culture from the virus, dry it in a vacuum, and spray-coated it with a thin silver atom layer. It is a good conductor and can help measure quantum tunneling. As a result, the scientists see in pictures the virus “landscape” with different values of tunneling current. Next, an image is split into small fragments and being studied.

It is known that the virus surface consists of lipids (“bricks” for any cell wall) — they are well-researched, and we did not have to recreate them. Our main goal was to study spike proteins. We really didn’t know much about how they looked.

That’s why also checked the data from an X-ray microscope — X-ray crystallography of the virus. Because the length of γ-ray waves is comparable with the size of separate atoms; so, it is possible to recreate the structure of the virus protein atom by atom. After that, we recorded the information to a special structural PDB file.

We converted all that data into the 3D format as polygons and points and then reassembled them in Cinema4D. The animation and rendering were made using Redshift 3D+AE. In the video, we showed how the virus gets into a cell.

In other words, we possessed finished drawings, and our goal was to assemble a realistic simulation based on them and check it. We also needed to choose the color of the virus.

Sure, at such a scale, we could not know its actual color. So we decided to paint it as we liked. First, we painted it blue and orange. Then we realized that the virus did not look aggressive enough in that colors. And we decided on a more disturbing palette: red, pink, and violet. We wanted to demonstrate that the virus is not something good, but it is beautiful and symmetrical.

We wanted to attract attention to it. The picture should say to anybody who sees it: “I am a dangerous virus, remember me well because we will spend together the next 100 years.”

Was it the first visualization of the virus at all?

Many teams were working on it. I know about one from India who created a very famous video about coronavirus. For example, Visual Science developed a high-quality model, but after us. And it shows the virus DNA in detail.

You should know that coronavirus can be depicted in different ways, and every image of it, if it is scientifically proven, would be correct. You can draw the virus as a human — schematically or photo-realistically.

Our detailed picture is something between a photorealistic image and a drawing in pencil. We have shown very precisely spike proteins and the membrane lipids less precisely (but they are not so important because they were studied a long time ago).

So you can say we were among the first. We made a 3D visualization in winter 2020. But we might not show it for a long time due to NDA. As we were allowed to publish it in spring 2021, there were already many similar visualizations presented. But I can assure you that our visualization was well-known among professional scientists and visualizers. This pic, for example, was printed in the almanac of the Association of Medical Illustrators (AMI) — a catalog of world achievements in the field of medical visualizations:

Who needs such a visualization?

First, it is scientifically proven because the depicted spike proteins are 100% the same as they look in nature. It is very significant for physicians to understand how it works because not all know how big is an antibody and how big is the virus. In our video, you can see how big the antibodies are, where they are attached to the virus, why the virus is not encapsulated by a cell, etc.

Such visualizations help scientists to understand the structure and active components of the virus. Plus, you can simulate some situations with a 3D model. For example, if a researcher studies compounds (molecules attached to the targets) for coronavirus, he can find out, using simulation, how his solution would work.

If a company came to us and asked to check a homeopathic medicines against coronavirus, create a video about how it works, we would refuse that offer because in that case, a video would show only floating coronavirus without any substance molecules around 🙂

Our visualizations show scientists the things based on microscopy data that you can’t see just with your eyes. We create models that allow us to check hypotheses and perform simulations. They show us how things are working actually.