# Application to Nextmol

From Alexey Nesterenko, PhD
Federal Center of Brain Research & Neurotechnologies
115093 Moscow, B.Serpukhovskaya 56/17

**Dear members of the search committee!**

I am writing to express my interest in your position of Senior R&D Engineer for Computational Modelling of Polymer Chemistry.

My experience covers a very broad spectrum of scientific problems in fields of computational biology/chemistry as you may see in my publication list. However the significant part of my projects including PhD thesis was in the field of computational chemistry and, in certain cases, in simulating polymers. Back in 2007, my graduation diploma was devoted to molecular-dynamics simulation of lateral proton diffusion at the membrane-water interface. So I started to work in computational chemistry from the very beginning of my scientific career.

In graduate school, I continued studying lipid bilayer via MD methods: we characterized electric double layer structure at the membrane-water interface by MD simulations. As a result, we successfully connected electrokinetic measurements in liposome suspension (zeta potential) with surface potential calulated from MD trajectories. Using Gouy-Chapman-Stern theory we learned how to calculate cation adsorption constant and binding capacity, which can be directly compared to electrokinetic measurements in liposome suspension. Finally, my PhD thesis was built at the boundary between theoretical colloid chemistry and computational chemistry.

After defence in 2014, I studied polycation interaction to DNA and lipid membranes with Prof. A.Gurtovenko and published two papers with him in 2016 (Kondinskaya et al., 2016; Kostritsky et al., 2016). Here, I built the naturalistic model for the polymers of interest and calculated partial charges by *ab initio* calculations of differently protonated oligomeric blocks. In 2015-16, I worked with MD models of carbohydrate polymers in the frame of the lipopolysaccharide (LPS) research project: we studied both O-antigen oligosaccharide chain separately in different force fields (Galochkina et al, 2016) and LPS-containing membranes (Orekhov et al, 2018; Galochkina et al, 2015). I understand that carbohydrates are very specific polymers, but I liked these studies and I hope that this experience could be utilized in Nextmol.

I also have experience in industry: I worked as a web-developer in 2007-8 in e-commerce, I worked as a sole enterpreneur developing instruments for electrophysiology, and performed individual orders in computational chemistry for Russian biotech companies. My academic experience is much bigger but I have always been interested in performing research closer to implementation. Your company looks very perspective in this context, and I hope that I can fruitfuly work on it and help international industry in creation of new molecules for materials and drugs.

I satisfy almost all the requirements mentioned for the candidate in the offer except thermodynamic modelling, LAMMPS and neural networks. I additionaly want to mention that I have experience with QM/MM and QM computations of periodic systems with plane-wave DFT approach implemented in CP2K (Ramazanov et al., 2016). My experience in data science was achieved in last two years during my work in FCBRN in the field of mass-spectrometry data analysis. Specificity of our tasks shifted my data science experience to the statistical learning. My programming skills and teaching experience are explicitly listed in the CV.

Finally, I hope that my broad experience would find an asset for your company. Anyway, thank you for your time and consideration; I look forward to speaking with the board about this employment opportunity.

Best regards,
Alexey Nesterenko

## References

**Dr. Andrey Gurtovenko**
Professor

Institute of Macromolecular Compounds, Russian Academy of Sciences
V.O. Bolshoi pr. 31, 199004 Saint-Petersburg, Russia
Phone: [phone], Mail: [e-mail]

**Dr. Philipp S. Orekhov**
Associate professor, Faculty of Biology

Shenzhen MSU-BIT University
No.1, International University Park Road, Longgang District, Shenzhen,
518172 Guangdong Province, PRC
Tel.: [phone], Mail: [e-mail]

**Dr. Tatiana Galochkina**
Assistant Professor in Structure Bioinformatics

Team 2, UMRS 1134 Inserm et Université de Paris
6 rue Alexandre Cabanel, 75015 Paris, France
Tel.: [phone], Mail: [e-mail]

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