LiveCoMS Roundtable: Discussing Markov state models after two decades of development v1.0
Abstract
Markov state models (MSMs) play a central role in the analysis of molecular dynamics (MD) simulations for biomolecules, and MSM methodologies have been under continual development since their introduction to the field in the early 2000s. MSMs take MD trajectory data as input and produce a more compact, i.e., coarse-grained, and interpretable representation of the system in terms of conformational states and quantitative observables such as the equilibrium populations of states and the timescales of interconverting between states. Numerous strategies and considerable mathematical formalism have been developed to improve coarse-graining in both time and space to enable the most reliable representation of the underlying biomolecular dynamics. Nevertheless, there remains considerable discussion in the literature regarding best practices and MSM limitations, as well as proposals to abandon or extend the first-order Markovian framework in common use. This Roundtable article gathers together diverse opinions from > 10 authors active in MSM development, and by design, each author or author group offers a separate contribution. No consensus view is provided. Instead, the article is meant to be a guide for readers wishing to be exposed to a wide set of expert perspectives.
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BibTeX
@misc{zuckerman2026livecoms,
title = {{LiveCoMS Roundtable: Discussing Markov state models after two decades of development v1.0}},
author = {Daniel M. Zuckerman and Gregory R. Bowman and Amedeo Caflisch and Aaron R. Dinner and Ahmed Fadhluddin and Giuseppe Giangreco and Xuhui Huang and Bettina G. Keller and Stefan Klus and Feliks Nüske and Michael O'Connor and Edina Rosta and Christof Schütte and Gerhard Stock and Vincent Voelz and Jonathan Weare and Antonia S. J. S. Mey},
howpublished = {arXiv},
year = {2026},
month = oct,
doi = {10.48550/arxiv.2610.24144},
eprint = {2610.24144},
archivePrefix = {arXiv},
url = {https://arxiv.org/abs/2610.24144},
note = {CC BY 4.0},
}
RIS
TY - UNPB
TI - LiveCoMS Roundtable: Discussing Markov state models after two decades of development v1.0
AU - Daniel M. Zuckerman
AU - Gregory R. Bowman
AU - Amedeo Caflisch
AU - Aaron R. Dinner
AU - Ahmed Fadhluddin
AU - Giuseppe Giangreco
AU - Xuhui Huang
AU - Bettina G. Keller
AU - Stefan Klus
AU - Feliks Nüske
AU - Michael O'Connor
AU - Edina Rosta
AU - Christof Schütte
AU - Gerhard Stock
AU - Vincent Voelz
AU - Jonathan Weare
AU - Antonia S. J. S. Mey
PY - 2026
DA - 2026/10/16
PB - arXiv
DO - 10.48550/arxiv.2610.24144
UR - https://arxiv.org/abs/2610.24144
AB - Markov state models (MSMs) play a central role in the analysis of molecular dynamics (MD) simulations for biomolecules, and MSM methodologies have been under continual development since their introduction to the field in the early 2000s. MSMs take MD trajectory data as input and produce a more compact, i.e., coarse-grained, and interpretable representation of the system in terms of conformational states and quantitative observables such as the equilibrium populations of states and the timescales of interconverting between states. Numerous strategies and considerable mathematical formalism have been developed to improve coarse-graining in both time and space to enable the most reliable representation of the underlying biomolecular dynamics. Nevertheless, there remains considerable discussion in the literature regarding best practices and MSM limitations, as well as proposals to abandon or extend the first-order Markovian framework in common use. This Roundtable article gathers together diverse opinions from > 10 authors active in MSM development, and by design, each author or author group offers a separate contribution. No consensus view is provided. Instead, the article is meant to be a guide for readers wishing to be exposed to a wide set of expert perspectives.
ER -