Daldrop, J.O. and Kappler, J. and Brünig, F.N. and Netz, R.R. (2018) Butane dihedral angle dynamics in water is dominated by internal friction. SFB 1114 Preprint 01/2018 . pp. 16. (Unpublished)

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Abstract
The dihedral dynamics of butane in water is known to be rather insensitive to the water viscosity, possible explanations for this involve inertial effects or Kramers’ turnover, the finite memory time of friction, and the presence of socalled internal friction. In order to disentangle these factors, we introduce a method to directly extract the friction memory function from simulations in the presence of an arbitrary freeenergy landscape. By analysis of the dihedral friction in butane for varying water viscosity, we demonstrate the existence of an internal friction contribution. At normal water viscosity the internal friction turns out to be eight times larger than the solvent friction and thus completely dominates the effective friction. By comparison with simulations of a constrained butane molecule that has the dihedral as the only degree of freedom, we show that internal friction comes from the six additional degrees of freedom in unconstrained butane that are orthogonal to the dihedral angle reaction coordinate. While the insensitivity of butane’s dihedral dynamics to water viscosity is solely due to the presence of internal friction, inertial effects nevertheless crucially influence the resultant transition rates. In contrast, nonMarkovian effects due to the finite memory time are present but do not significantly influence the dihedral barrier crossing rate of butane. These results not only settle the character of dihedral dynamics in small molecular systems such as butane, they also have important implications for the folding of polymers and proteins
Item Type:  Article 

Subjects:  Mathematical and Computer Sciences > Mathematics > Applied Mathematics 
ID Code:  2225 
Deposited By:  Silvia Hoemke 
Deposited On:  21 Feb 2018 10:35 
Last Modified:  22 Feb 2018 13:09 
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