This repository contains code to reproduce numerical simulations and visualizations of Tim Hempel, Mauricio J. del Razo, Christopher T. Lee, Bryn C. Taylor, Rommie E. Amaro, and Frank Noé: Independent Markov Decomposition: Toward Modeling Kinetics of Biomolecular Complexes, Proc Natl Acad Sci USA 2021, 118 (31), e2105230118. https://doi.org/10.1073/pnas.2105230118.
(Pre-print version: https://www.biorxiv.org/content/10.1101/2021.03.24.436806v1)
Demonstrates combinatorial explosion of global states vs. independent Markov decomposition. Reproduces Fig. 1 in the manuscript.
Implementation of Hodgkin-Huxley potassium ion channel model and numerical simulation of the dynamics. Reproduces Fig. 3c and d in the manuscript.
Implementation of coupled ion channel dimer and numerical simulation of the dynamics at various coupling strenghts. Reproduces Fig. 4 c and d in the manuscript.
Dependency graph estimation and visualization for MD data of Synaptotagmin-C2A domain. Reproduces Fig. 5a in the manuscript.
Assessment of limited sampling effects using a simple toy model. Reproduces Fig. S1 in the supplemental material.
Counterexample to IMD with small peptide Chignolin (10 amino acids). Reproduces Fig. S3 in the supplemental material.