Berke
Türkaydin

Executed extensive multi-microsecond molecular dynamics simulations (including OPES-enhanced sampling) of TREK K2P channel constructs to map the free-energy landscape of gating and conduction states. Developed and validated custom collective variables and used kernel-based reweighting to extract high-resolution free-energy surfaces differentiating up- and down-states of the channel. Designed and implemented high-throughput simulation workflows on several different HPC environments and cloud-based simulation infrastructure. Executed protein-ligand MD simulations to understand atomistic effect and stability of small molecules. Parameterized phosphorylation mimics and lipid-tether modifications to probe how the cytosolic proximal C-terminus (pCt) couples with the selectivity filter (SF), and demonstrated two distinct allosteric pathways controlling ion conduction. Worked closely with experimental collaborators, communicated simulation results to electrophysiologists.

Applied machine learning workflows to extract high-value structural features from large-scale MD simulations of membrane proteins and ion channels. Built PyTorch-based models for dimensionality reduction (autoencoders / tICA-inspired networks) and clustering to identify hidden conformational states and transition pathways. Integrated RDKit to engineer chemical and molecular descriptors, improving ligand-recognition features and enhancing interpretation of protein–ligand trajectories. Used ML-driven insights to optimize MD simulations, including: selecting more informative collective variables, initializing enhanced-sampling runs from ML-identified metastable states, prioritizing sampling regions predicted to impact energetic barriers.

Performed extensive OPES-enhanced MD simulations to explore the free-energy landscape of TREK K2P ion channels and understand allosteric coupling mechanisms. Designed and optimized collective variables to capture functionally relevant conformational transitions. Applied kernel reweighting and advanced analysis pipelines to reconstruct accurate free-energy surfaces. Identified structural pathways through which phosphorylation, membrane-stretch and a disease mutant modulates gating and channel dynamics. Communicated mechanistic insights to interdisciplinary collaborators and contributed to manuscript development.