Freie Universität Berlin
Fachbereich Mathematik und Informatik
German Research Foundation (DFG)
Mechanisms of ion channel regulation investigated by extensive simulation and Markov state modeling
The DFG Research Unit initiative "DynIon - Functional dynamics of ion channels and transporters" combines experimental and computational strategies to study ion channels and transporters. In this project, we will provide our expertise in long-timescale simulation and Markov state modeling from both experimental and simulation data to the research unit. By combining extensive GPU-driven MD simulations (100 microsecond to milliseconds) with recently developed adaptive sampling techniques and multi-ensemble estimators, we will explore the conformational dynamics of binding domains in AMPA-type glutamate receptors and their modulation by binding auxiliary proteins. Methodologically, we will develop new Bayesian inference methods to learn MSMs from single-channel data and optimally combine them with simulation data.