Dynamic coupling between coordinates in a model for biomolecular isomerization

The Journal of Chemical Physics
Ao MaAaron R Dinner

Abstract

To understand a complex reaction, it is necessary to project the dynamics of the system onto a low-dimensional subspace of physically meaningful coordinates. We recently introduced an automatic method for identifying coordinates that relate closely to stable-state commitment probabilities and successfully applied it to a model for biomolecular isomerization, the C(7eq)-->alpha(R) transition of the alanine dipeptide [A. Ma and A. R. Dinner, J. Phys. Chem. B 109, 6769 (2005)]. Here, we explore approximate means for estimating diffusion tensors for systems subject to restraints in one and two dimensions and then use the results together with an extension of Kramers theory for unimolecular reaction rates [A. Berezhkovskii and A. Szabo, J. Chem. Phys. 122, 014503 (2005)] to show explicitly that both the potential of mean force and the diffusion tensor are essential for describing the dynamics of the alanine dipeptide quantitatively. In particular, the signficance of off-diagonal elements of the diffusion tensor suggests that the coordinates of interest are coupled by the hydrodynamic-like response of the bath of remaining degrees of freedom.

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Citations

Mar 21, 2008·Proceedings of the National Academy of Sciences of the United States of America·Jie HuAaron R Dinner
Feb 15, 2013·The Journal of Chemical Physics·Baron PetersJoan-Emma Shea
Dec 3, 2008·The Journal of Chemical Physics·Maria Mills, Ioan Andricioaei
Aug 7, 2009·The Journal of Chemical Physics·Sergio BacalladoVijay Pande
Jun 7, 2012·The Journal of Chemical Physics·Masao Iwamatsu
Feb 27, 2008·The Journal of Chemical Physics·Ying LiAaron R Dinner
Apr 17, 2009·The Journal of Chemical Physics·Christopher P CalderonIoan Kosztin
Sep 27, 2006·The Journal of Chemical Physics·Jie HuAaron R Dinner
Sep 10, 2014·Molecular Simulation·Wenjin Li, Ao Ma
May 16, 2009·Journal of Computational Chemistry·B R BrooksM Karplus
Dec 24, 2018·The Journal of Chemical Physics·Ronaldo Junio de Oliveira
Jul 1, 2019·The Journal of Chemical Physics·Erik H ThiedeJonathan Weare
Sep 7, 2020·The Journal of Chemical Physics·Huiyu Li, Ao Ma
Dec 12, 2012·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Masao Iwamatsu
Mar 18, 2021·Journal of Chemical Theory and Computation·François SicardEdina Rosta
May 5, 2010·The Journal of Physical Chemistry. B·Bo QiAaron R Dinner
Aug 29, 2009·The Journal of Physical Chemistry. B·Igor V KalginSergei F Chekmarev
Aug 19, 2021·The Journal of Physical Chemistry. B·Subhajit AcharyaBiman Bagchi
Jan 14, 2020·The Journal of Physical Chemistry Letters·Frederico Campos Freitas, Ronaldo Junio de Oliveira
Oct 15, 2021·The Journal of Physical Chemistry. B·Adam AntoszewskiAaron R Dinner

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