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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)

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