About Me

I'm a researcher in the fields of molecular biology, structural biology, biochemistry and biophysics dedicated to unraveling the complexities of molecular structures. Here, you can explore my journey, discoveries, and insights into my pathway.

Official Curriculum Vitae

Informal Curriculum Vitae

Vladimir Arinkin next to Titan Krios electron microscope

Vita

At the University of Geneva, I took a staff scientist position. I got more opportunities to train and supervise, preparing me for my future independent position. I am also continuing my Cryo-EM journey, thanks to Jacques Dubochet's legacy from EMBL to the Dubochet Centre for Imaging unit in Geneva. Meanwhile, I am advancing in expanding my biophysics repertoire with SEC-MALS, nanoDSF, and thermophoresis. I am meticulously exploring all the details of eukaryotic expression systems to design new in vivo fluorescence-based assays.

Moreover, I could not overlook the great development of AlphaFold 3, which can predict 3D protein-DNA structures. Naturally, I immediately launched predictions for the unknown states of transposases, but nothing convincing came out. Still, it is a great tool for many cases and can definitely be used for hypothesis generation

For my PostDoc, I headed to EMBL, which I can describe as Europe within a campus. From working on optogenetic tools, I leaped into the DNA world, particularly focusing on a peculiar area: transposases - enzymes that move their own coding DNA within the genome or even escape the host; can I call it "DNA self-propulsion"? This was a new challenge, as these proteins are not under evolutionary pressure to be the best enzymes - they are too deleterious for the host if too active, needing just enough efficiency to spread.

One of them, Sleeping Beauty, had evaded DNA-bound structure determination for decades despite its wide applied use. Many approaches had been tried before, but I took on the challenge. It was rewarding to see the beautiful structure of Sleeping Beauty.

Along the way, I ventured into new territories, including insect and mammalian cell culture, biochemical assays, and flow cytometry. The resolution revolution in Cryo-EM had not gone unnoticed by me. I freely plunged into water vitrification at EMBL, at the facility which has original Jacques Dubochet plunger.

My fascination with proteins and fluorescence microscopy led me to the structural biology of fluorescent proteins. After dozens of hours spent in darkness filled with dim red light, seeing my first protein crystal structure had a "wow" effect. Yet, I quickly realised that it's just a snapshot of living molecules, which prompted me to delve into spectroscopy, quantum mechanical calculations and molecular dynamics simulations.

A new avenue opened with structural work on optogenetic tools. It was fascinating that one could control molecular processes with light...

I stumbled upon an open position for a physicist willing to dive into biophysics, related to water, phase transitions, and cellular biophysics. At 19 years old, with one piece of luggage and 500 Euros in my pocket, I departed to start a new chapter as a research assistant in Germany.

It was exciting to study the biophysics of red blood cells, which have high amounts of hemoglobin, yet cells become more fluid after a phase transition around elevated body temperature.

Thanks to my supervisor, I was able to start my master's studies in parallel with my research assistant position. For my master's thesis, I plunged into a new area of plant phenotyping using fluorescence microscopy, spectroscopy, image analysis crowned by neural network-based analysis (today it would all just be called AI).

I got excited about Physics, thanks to my beloved father, and joined the Physics department. The first lecture by an inspiring physicist left an indelible impression on me, filled with so much thoughtfulness and attention to details. Together with others, they taught us the most important thing in science: to ask questions of nature and find ways to read the answers.

For my thesis, I found an exciting opportunity to study WATER! Check this Waterpedia! Who would have thought that it has more than 20 phase states! Sometimes I think it must be at least a prototype of alkahest.