Related papers: Monomer motion in single- and double-stranded DNA …
The accurate knowledge of the elastic properties of single-stranded DNA (ssDNA) is key to characterize the thermodynamics of molecular reactions that are studied by force spectroscopy methods where DNA is mechanically unfolded. Examples…
Motivated by the experiments on DNA under torsion, we consider the problem of pulling a polymer out of a potential well by a force applied to one of its ends. If the force is less than a critical value, then the process is activated and has…
Single-molecule experiments in which force is applied to DNA or RNA molecules have enabled important discoveries of nucleic acid properties and nucleic acid-enzyme interactions. These experiments rely on a model of the polymer…
The dynamics of flexible polymer molecules are often assumed to be governed by hydrodynamics of the solvent. However there is considerable evidence that internal dissipation of a polymer contributes as well. Here we investigate the dynamics…
We provide a Boltzmann-type kinetic description for dilute polymer solutions based on two-fluid theory. This Boltzmann-type description uses a quasi-equilibrium based relaxation mechanism to model collisions between a polymer dumbbell and a…
A theory of the unzipping of double-stranded (ds) DNA is presented, and is compared to recent micromanipulation experiments. It is shown that the interactions which stabilize the double helix and the elastic rigidity of single strands (ss)…
In order to study rheological properties of gelling systems in dilute solution, we investigate the viscosity and the normal stresses in the Zimm model for randomly crosslinked monomers. The distribution of cluster topologies and sizes is…
Overstretching of B-DNA is currently understood as force-induced melting. Depending on the geometry of the stretching experiment, the force threshold for the overstretching transition is around 65 or 110 pN. Although the mechanisms behind…
We present a detailed study of the static and dynamic behavior of long semiflexible polymer chains in a melt. Starting from previously obtained fully equilibrated high molecular weight polymer melts [{\it Zhang et al.} ACS Macro Lett. 3,…
The Rouse-Zimm equation for the position vectors of beads mapping the polymer is generalized by taking into account the viscous aftereffect and the hydrodynamic noise. For the noise, the random fluctuations of the hydrodynamic tensor of…
The aim of the present paper is the study of the entropic elasticity of the dsDNA molecule, having a cristallographic length L of the order of 10 to 30 persistence lengths A, when it is subject to spatial obstructions. We have not tried to…
Advances in controlled polymerization have enabled the synthesis of mechanically interlocked polymers like molecular knots and linear[n]catenane. These aesthetic macromolecules with unique topological constraints in the form of mechanical…
We study the equilibrium dynamics of a single polymer chain under good solvent condition. Special emphasis is laid on varying the drag force experienced by the chain while it moves. To this end we model the solvent in a mesoscopic manner by…
We discuss simulations of a simple model for polymer blends in the framework of the Rouse model. At odds with standard predictions, large dynamic asymmetry between the two components induces strong non-exponentiality of the Rouse modes for…
Three coarse-grained models of the double-stranded DNA are proposed and compared in the context of mechanical manipulation such as twisting and various schemes of stretching. The models differ in the number of effective beads (between two…
The phase behaviour of a single large semiflexible polymer immersed in a suspension of spherical particles is studied. All interactions are simple excluded volume interactions and the diameter of the spherical particles is an order of…
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…
In this study, we investigate the suitability of dissipative particle dynamics (DPD) simulations to predict the dynamics of polymer chains in dilute polymer solutions, where the chain is represented by a set of beads connected by almost…
In this paper, we present a theory to efficiently deal with mechanical properties of heterogeneous polymer chain in free space and the central problem is to evaluate the diffusion equation and orientation-orientation correlation function,…
DNA and other biopolymers differ from classical polymers due to their torsional stiffness. This property changes the statistical character of their conformations under tension from a classical random walk to a problem we call the `torsional…