Berk A. Alpay

PyKappa is a Python package for rule-based modeling that enables interactive simulation and analysis, including with agentic AI, demonstrated through a phase separation case study.

The paper performs a statistical meta-analysis of single amino acid substitutions using deep mutational scans to quantify physicochemical trends and derive an empirical amino acid exchangeability matrix.

This study examines how selection stringency affects outcomes in directed evolution by analyzing fitness distributions and diversification effects across rounds.