Department: Chemistry Faculty Adviser: William Jacobs Year of Study: G5 Undergraduate School: MIPT (Moscow) Undergraduate Major: Applied math and physics
More info: https://polyachenkoya.github.io/ I started doing research in high school. I wrote a stellar dynamics program to simulate a galaxy and studied the formation of spiral structures in galaxies. In my undergrad (at MIPT, Moscow), I worked in the lab "Computational Methods in Condensed Matter Physics". My first project was about a specific correlator that allowed finding transition temperatures using relatively small simulation boxes (meaning fewer computational resources). The second project was to verify a certain molecular-dynamical model of crystalline lysozyme protein by comparing the computed and experimentally measured stress modulus of the system. A crystalline phase is required for X-ray protein structural studies, yet there is a lack of accurate force fields describing crystalline protein behavior. My master's project was done at EPFL (Switzerland). I was simulating translocations of proteins through the Aerolysin nanopore. Nanopore sequencing is a relatively new field that has been developed in Oxford, U Illinois, EPFL, and many other places. In summer 2025, I looked outside of biophysics by doing a materials science project at PPPL. I ran quantum-level molecular dynamics to study plasma processing of certain quasi-2D materials that may be a promising substitute for Silicon in microelectronics. Last summer (2026), I added to the BoltzGen gen-AI model by developing a physics-inspired approach to use inference-time guidance of generative diffusion protein models to generate stable proteins more efficiently. Besides research (which I genuinely enjoy), I am into outdoor activities. I like hiking, swimming, climbing, and sometimes running. I am also interested in psychology, sociology, and philosophy. I think people are no less interesting than molecules to study.
I really liked my winter trip to Baikal - the deepest lake in the world.
My main PhD project a study of the early stages of DNA transcription. It was shown ~15 years ago that protein aggregates are essential for inter-nuclear processes in living cells. I am running computer simulations of how protein condensates form on DNA to facilitate transcription. We found a regime where transcriptional condensates are perfectly targeted to transcription regions, which is exactly what a cell wants. My most recent project is about extending the use of inference-time guidance of protein gen-AI models to other properties beyond protein stability. Another project is in materials science in collaboration with PPPL. We are investigating the use of low-energy plasma in the processing of quasi-2D materials, specifically transition metal dichalcogenides (TMDs). These materials are a promising substitution for Silicon in microchips because making Si transistors too small breaks the favorable Si properties, while these TMDs are naturally atomically thin. Low-energy plasmas, i.e. bombardment with low-energy ions, can be used to controllably introduce nucleation sites to grow TMDs, to substitute parts of a TMD with other atoms, to clean TMDs from oxidation, and more. We are doing quantum-level computer simulations (mostly DFT) of a TMD impacted by plasma ions to study the damage details.
Interested in participating in Summer 2027 ReMatch+ program.
