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Compression algorithms reveal memory effects and static disorder in single-molecule trajectories

Kevin Song1, Dmitrii E. Makarov2,3,*, and Etienne Vouga1

  • 1Department of Computer Science, University of Texas at Austin, Austin, Texas 78712, USA
  • 2Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, USA
  • 3Oden Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, USA

  • *makarov@cm.utexas.edu

Reliability of a nonlinear fluctuation-dissipation relation as a test of Markovianity

Georg Podhaisky, Igor M. Sokolov, Yael Roichman, and Benjamin Lindner

Phys. Rev. E 113 044130 (2026)

Uncovering dissipation from coarse observables: A case study of a random walk with unobserved internal states

Oleg A. Igoshin, Anatoly B. Kolomeisky, and Dmitrii E. Makarov

The Journal of Chemical Physics 162 034111 (2025)

Towards Markov-state holography

Xizhu Zhao, Dmitrii E Makarov, and Aljaž Godec

New J. Phys. 27 125002 (2025)

High-order Michaelis-Menten equations allow inference of hidden kinetic parameters in enzyme catalysis

Divya Singh, Tal Robin, Michael Urbakh, and Shlomi Reuveni

Nat Commun 16 2739 (2025)

Model-free photon analysis of diffusion-based single-molecule FRET experiments

Ivan Terterov, Daniel Nettels, Tanya Lastiza-Male, Kim Bartels, Christian Löw, Renee Vancraenenbroeck, Itay Carmel, Gabriel Rosenblum, and Hagen Hofmann

Nat Commun 16 5537 (2025)

Information-theoretical limit on the estimates of dissipation by molecular machines using single-molecule fluorescence resonance energy transfer experiments

Kevin Song, Dmitrii E. Makarov, and Etienne Vouga

The Journal of Chemical Physics 161 044111 (2024)

Milestoning estimators of dissipation in systems observed at a coarse resolution

Kristian Blom, Kevin Song, Etienne Vouga, Aljaž Godec, and Dmitrii E. Makarov

Proc. Natl. Acad. Sci. U.S.A. 121 e2318333121 (2024)

Single-molecule FRET for probing nanoscale biomolecular dynamics

Daniel Nettels, Nicola Galvanetto, Miloš T. Ivanović, Mark Nüesch, Tianjin Yang, and Benjamin Schuler

Nat Rev Phys 6 587 (2024)

Non-Markov models of single-molecule dynamics from information-theoretical analysis of trajectories

Kevin Song, Raymond Park, Atanu Das, Dmitrii E. Makarov, and Etienne Vouga

The Journal of Chemical Physics 159 064104 (2023)

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