The effect of a slit-like confinement on the relaxation dynamics of DNA is studied via a mesoscale model in which a bead and spring model for the polymer is coupled to a particle-based Navier-Stokes solver (multi-particle collision dynamics). The confinement is found to affect the equilibrium stretch of the chain when the bulk gyration radius is comparable to or smaller than the channel height and our data are in agreement with the (R(g,bulk)/h)(1/4) scaling of the polymer extension in the wall tangential direction. Relaxation simulation at different confinements indicates that, while the overall behaviour of the relaxation dynamics is similar for low and strong confinements, a small, but significant, slowing of the far-equilibrium relaxation is found as the confinement increases.

Chinappi, M., De Angelis, E. (2011). Confined dynamics of a single DNA molecule. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY OF LONDON SERIES A: MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 369(1944), 2329-2336 [10.1098/rsta.2011.0096].

Confined dynamics of a single DNA molecule

Chinappi M.;
2011-01-01

Abstract

The effect of a slit-like confinement on the relaxation dynamics of DNA is studied via a mesoscale model in which a bead and spring model for the polymer is coupled to a particle-based Navier-Stokes solver (multi-particle collision dynamics). The confinement is found to affect the equilibrium stretch of the chain when the bulk gyration radius is comparable to or smaller than the channel height and our data are in agreement with the (R(g,bulk)/h)(1/4) scaling of the polymer extension in the wall tangential direction. Relaxation simulation at different confinements indicates that, while the overall behaviour of the relaxation dynamics is similar for low and strong confinements, a small, but significant, slowing of the far-equilibrium relaxation is found as the confinement increases.
2011
Pubblicato
Rilevanza internazionale
Articolo
Esperti anonimi
Settore ING-IND/06 - FLUIDODINAMICA
Settore ING-IND/34 - BIOINGEGNERIA INDUSTRIALE
English
polymer dynamics; confinement effects; multi-particle collision dynamics
Chinappi, M., De Angelis, E. (2011). Confined dynamics of a single DNA molecule. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY OF LONDON SERIES A: MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 369(1944), 2329-2336 [10.1098/rsta.2011.0096].
Chinappi, M; De Angelis, E
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2108/247415
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