A generalized bead-rod model for Brownian dynamics simulations of wormlike chains under strong confinement

Abstract

This paper is aimed to develop a Brownian dynamics simulation method for strongly confined semiflexible polymers where numerical simulation plays an indispensable role in complementing theory and experiments. A wormlike chain under strong confinement is modeled as a string of virtual spherical beads connected by inextensible rods with length varying according to the confinement intensity of the chain measured by the Odijk deflection length. The model takes hydrodynamic interactions into account. The geometrical constraints associated with the inextensible rods are realized by the so-called linear constraint solver. The model parameters are studied by quantitatively comparing the simulated properties of a double-stranded DNA chain with available experimental data and theoretical predictions.

Evaluation of the Kirkwood approximation for the diffusivity of channel-confined DNA chains in the de Gennes regime

“…This model breaks down in stronger confinement because it is unable to resolve the chain configurations at the length scale of a persistence length. There are other options to model polymers in such strong confinement, such as the touching-bead model 48 that we have used previously in our studies of the Kirkwood diffusivity of DNA in confinement. 13 Unfortunately, dynamic simulations of the touching-bead model would likely require simulating thousands of beads to reach the long-chain limit.…”

Mixed confinement regimes during equilibrium confinement spectroscopy of DNA

“…27,41 The model consists of a discretized chain of contour length L with N b + 1 beads connected by rigid rods of length l b . The bond angles between the rods are constrained using the bending potential…”

DNA confined in nanochannels: Hairpin tightening by entropic depletion

“…An analytical solution of the relevant Fokker-Planck equation for a stiff chain trapped in a pore, which addresses all fluctuations, is well known to be difficult, although numerical analyses have been performed. [34][35][36][37][38][39][40] My emphasis will be on an analysis of this phenomenon in the mechanical limit for the hairpin curve. The hairpin will be assumed to be a two-dimensional curve within a plane aligned along the long axis of the nanochannel.…”