Related papers: Unwinding relaxation dynamics of polymers
We study the Langevin dynamics of diffusive particles with regular pairwise interactions under mean-field scaling. By approximating empirical distributions with conditional distributions, we establish coercive and contractive properties for…
The importance of nonlinearities in material constitutive relations has long been appreciated in the continuum mechanics of macroscopic rods. Although the moment (torque) response to bending is almost universally linear for small deflection…
We study numerically the mechanical stability and elasticity properties of duplex DNA molecules within the frame of a network model incorporating microscopic degrees of freedom related with the arrangement of the base pairs. We pay special…
We present a generic coarse-grained model to describe molecular motors acting on polymer substrates, mimicking, for example, RNA polymerase on DNA or kinesin on microtubules. The polymer is modeled as a connected chain of beads; motors are…
Nonequilibrium molecular dynamics simulations are used to study the deformation behavior of disperse polymer melts by tracking test chains of length N = Mw, the weight average molecular weight, in melts of varying dispersity. At high strain…
We investigate by Monte Carlo simulations the zipping and unzipping dynamics of two polymers connected by one end and subject to an attractive interaction between complementary monomers. In zipping, the polymers are quenched from a high…
We perform two-dimensional Langevin dynamics simulations of electric-field driven polymer translocation through an attractive nanopore. We investigate the effect of the location of the attractive region using different pore patterns. This…
We consider the hydrodynamics of lipid bilayers containing transmembrane proteins of arbitrary shape. This biologically-motivated problem is relevant to the cell membrane, whose fluctuating dynamics play a key role in phenomena ranging from…
The interaction of polymers with turbulent shear flows is examined. We focus on the structure of the elastic stress tensor, which is proportional to the polymer conformation tensor. We examine this object in turbulent flows of increasing…
The thermodynamic properties of DNA circular molecules are investigated by a new path integral computational method which treats in the real space the fundamental forces stabilizing the molecule. The base pair and stacking contributions to…
In this article we study from a non-perturbative point of view the entanglement of two directed polymers subjected to repulsive interactions given by a Dirac $\delta-$function potential. An exact formula of the so-called second moment of…
The breakage of a polymer chain of segments, coupled by anharmonic bonds with applied constant external tensile force is studied by means of Molecular Dynamics simulation. We show that the mean life time of the chain becomes progressively…
We present results from our simulations of biopolymer translocation in a solvent which explain the main experimental findings. The forced translocation can be described by simple force balance arguments for the relevant range of pore…
We study the translocation of a semiflexible polymer through extended pores with patterned stickiness, using Langevin dynamics simulations. We find that the consequence of pore patterning on the translocation time dynamics is dramatic and…
We present a dynamical model of DNA mechanical unzipping under the action of a force. The model includes the motion of the fork in the sequence-dependent landscape, the trap(s) acting on the bead(s), and the polymeric components of the…
Stretched polymers with attractive interaction are studied in two and three dimensions. They are described by biased self-avoiding random walks with nearest neighbour attraction. The bias corresponds to opposite forces applied to the first…
We consider the rupture dynamics of a homopolymer chain pulled at one end at a constant loading rate r. Compared to single bond breaking, the existence of the chain introduces two new aspects into rupture dynamics: the non-Markovian aspect…
The torsional dynamics of a semiflexible polymer with a contour length $L$ larger than its persistence length L_p that is rotated at fixed frequency omega_0 at one end is studied by scaling arguments and hydrodynamic simulations. We find a…
The force-level Elastically Collective Nonlinear Langevin Equation theory of activated relaxation in glass-forming free-standing thin films is re-visited to improve its treatment of collective elasticity effects. The naive cut off of the…
The some dynamic properties of a random heteropolymer in the condensed state are studied in the mode coupling approximation. In agreement with recent report a dynamic friction increasing is predicted for the random heteropolymer with…