Projects

In progress

A new model including the implicit water model and explicit was developed to simulate highly charged large systems that require enormous amounts of water to simulate. It shows the ability to reproduce ion distributions around DNA qualitatively correctly. Using the model we are to explore the behaviour of nucleosomes in different conditions to reveal the physical basis of epigenetic phenomena. The model is already available in AMBER package (Tutorial)

2023

I am interested in revealing the physical basis of the chromatin compaction. In particular, what exact physical processes and parameters allow cells to distinguish the genes needed to express and ones that should be silent for now?

Using MD simulations in the presence of PEG and a multi-shell model of ion-induced DNA condensation we have estimated the difference of DNA aggregation energy in solutions with NaCl and KCl. The probability of DNA aggregation in the presence of sodium is ~1.5 of an order higher than that of potassium. Our estimations allow us to explain experimental observations. *Picture is a link

2021

We have tested the ability of 3 widely used water models to represent the distributions of sodium and potassium ions around DNA. The most significant difference was found near the DNA helical axis. *Picture is a link

Past Experience and Education

BS Moscow Institute of Physics and Technology

Sep 2015 – Jun 2019

Bachelor of Science in biophysics. For the bachelor's project, I produced membrane protein A2A and assembled membrane nanodisks with the synthesized receptor.

MS Moscow Institute of Physics and Technology

Sep 2019 – Jun 2021

Master of Science in biophysics. The master project included the results of the article published in 2021 and the preliminary results of the work published in 2023.

Ph.D. Virginia Tech

Aug 2023 – May 2028

Assumed Ph.D. thesis will include results of the examination of effects of different parameters on DNA compaction into the nucleosome. In particular, how redistribution of ions due to DNA and protein modifications propagate DNA packaging.