Independent Markov decomposition

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)

Overview

Fig1-scaling-multiple-3state-systems.ipynb

Demonstrates combinatorial explosion of global states vs. independent Markov decomposition. Reproduces Fig. 1 in the manuscript.

Fig3cd-ion-channel-discrete-model.ipynb

Implementation of Hodgkin-Huxley potassium ion channel model and numerical simulation of the dynamics. Reproduces Fig. 3c and d in the manuscript.

Fig4cd-ion-channel-optimal-partition.ipynb

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.

Fig5a-syt-decomposition.ipynb

Dependency graph estimation and visualization for MD data of Synaptotagmin-C2A domain. Reproduces Fig. 5a in the manuscript.

FigS1-approximation-quality-2-2state-systems.ipynb

Assessment of limited sampling effects using a simple toy model. Reproduces Fig. S1 in the supplemental material.

FigS3-counterexample-Chignolin.ipynb

Counterexample to IMD with small peptide Chignolin (10 amino acids). Reproduces Fig. S3 in the supplemental material.