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Simulating a chemically fueled molecular motor with nonequilibrium molecular dynamics

Author

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  • Alex Albaugh

    (Northwestern University)

  • Todd R. Gingrich

    (Northwestern University)

Abstract

Most computer simulations of molecular dynamics take place under equilibrium conditions—in a closed, isolated system, or perhaps one held at constant temperature or pressure. Sometimes, extra tensions, shears, or temperature gradients are introduced to those simulations to probe one type of nonequilibrium response to external forces. Catalysts and molecular motors, however, function based on the nonequilibrium dynamics induced by a chemical reaction’s thermodynamic driving force. In this scenario, simulations require chemostats capable of preserving the chemical concentrations of the nonequilibrium steady state. We develop such a dynamic scheme and use it to observe cycles of a particle-based classical model of a catenane-like molecular motor. Molecular motors are frequently modeled with detailed-balance-breaking Markov models, and we explicitly construct such a picture by coarse graining the microscopic dynamics of our simulations in order to extract rates. This work identifies inter-particle interactions that tune those rates to create a functional motor, thereby yielding a computational playground to investigate the interplay between directional bias, current generation, and coupling strength in molecular information ratchets.

Suggested Citation

  • Alex Albaugh & Todd R. Gingrich, 2022. "Simulating a chemically fueled molecular motor with nonequilibrium molecular dynamics," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-29393-3
    DOI: 10.1038/s41467-022-29393-3
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    References listed on IDEAS

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    1. Hiroyuki Noji & Ryohei Yasuda & Masasuke Yoshida & Kazuhiko Kinosita, 1997. "Direct observation of the rotation of F1-ATPase," Nature, Nature, vol. 386(6622), pages 299-302, March.
    2. T. Ross Kelly & Harshani De Silva & Richard A. Silva, 1999. "Unidirectional rotary motion in a molecular system," Nature, Nature, vol. 401(6749), pages 150-152, September.
    3. Martin F. Engelke & Michael Winding & Yang Yue & Shankar Shastry & Federico Teloni & Sanjay Reddy & T. Lynne Blasius & Pushpanjali Soppina & William O. Hancock & Vladimir I. Gelfand & Kristen J. Verhe, 2016. "Engineered kinesin motor proteins amenable to small-molecule inhibition," Nature Communications, Nature, vol. 7(1), pages 1-12, September.
    4. Miriam R. Wilson & Jordi Solà & Armando Carlone & Stephen M. Goldup & Nathalie Lebrasseur & David A. Leigh, 2016. "An autonomous chemically fuelled small-molecule motor," Nature, Nature, vol. 534(7606), pages 235-240, June.
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