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Transition state theory demonstrated at the micron scale with out-of-equilibrium transport in a confined environment

Author

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  • Christian L. Vestergaard

    (Technical University of Denmark
    Present address: Aix Marseille Université, Université de Toulon, CNRS, CPT, UMR 7332, 13288 Marseille, France)

  • Morten Bo Mikkelsen

    (Technical University of Denmark)

  • Walter Reisner

    (Technical University of Denmark
    Present address: Department of Physics, McGill University, Montreal, Quebec, Canada H3A 2T8)

  • Anders Kristensen

    (Technical University of Denmark)

  • Henrik Flyvbjerg

    (Technical University of Denmark)

Abstract

Transition state theory (TST) provides a simple interpretation of many thermally activated processes. It applies successfully on timescales and length scales that differ several orders of magnitude: to chemical reactions, breaking of chemical bonds, unfolding of proteins and RNA structures and polymers crossing entropic barriers. Here we apply TST to out-of-equilibrium transport through confined environments: the thermally activated translocation of single DNA molecules over an entropic barrier helped by an external force field. Reaction pathways are effectively one dimensional and so long that they are observable in a microscope. Reaction rates are so slow that transitions are recorded on video. We find sharp transition states that are independent of the applied force, similar to chemical bond rupture, as well as transition states that change location on the reaction pathway with the strength of the applied force. The states of equilibrium and transition are separated by micrometres as compared with angstroms/nanometres for chemical bonds.

Suggested Citation

  • Christian L. Vestergaard & Morten Bo Mikkelsen & Walter Reisner & Anders Kristensen & Henrik Flyvbjerg, 2016. "Transition state theory demonstrated at the micron scale with out-of-equilibrium transport in a confined environment," Nature Communications, Nature, vol. 7(1), pages 1-9, April.
    • Handle: RePEc:nat:natcom:v:7:y:2016:i:1:d:10.1038_ncomms10227
    DOI: 10.1038/ncomms10227
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    Cited by:

    1. Zezhou Liu & Xavier Capaldi & Lili Zeng & Yuning Zhang & Rodrigo Reyes-Lamothe & Walter Reisner, 2022. "Confinement anisotropy drives polar organization of two DNA molecules interacting in a nanoscale cavity," Nature Communications, Nature, vol. 13(1), pages 1-12, December.

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