Dafina Marin-Gerdes
Biochemistry PhD Student, Marianski Lab
Hunter College – Expected Graduation: 2029
Objective
Looking for opportunities to collaborate on computational approaches to antibody engineering, including molecular modeling, molecular dynamics simulations, and machine learning. I am also interested in companies where my project and skills are transferable, and I am open to exploring career paths in industry or finance alongside academic research.
Bio
Dafina is a member of the Marianski Lab, where the focus is developing computational methods to improve antibody-based diagnostics and therapeutics. Her thesis project centers on identifying and modeling surface-accessible lysine environments on monoclonal antibodies to enable site-selective labeling. By applying molecular dynamics simulations, geometric deep learning tools such as MaSIF, and structure prediction platforms, she aims to classify lysine residues by their full local context—paving the way toward more predictable and reproducible antibody conjugates.
Outside of the lab, Dafina enjoys spending time with her family: cooking, walking, reading, and working on creative projects together.
Technical Skills
Molecular dynamics simulations (GROMACS, VMD), Structure prediction (AlphaFold2/3), Data visualization & analysis (Python, NumPy, Matplotlib), Bash scripting, PyMOL, Radial distribution function & H-bond analysis, Geometric deep learning tools (MaSIF)
Professional Development Skills
Publications
Conferences
Attended NanoBioNYC Symposium (2024)
Awards
NanoBioNYC Fellowship (2025)
CUNY Science Scholarship (2024-Present)

