Related papers: Stick-release pattern in stretching single condens…
In a recent experiment, a single DNA double helix is stretched and relaxed in the presence of spermidine, a short positive polyelectrolyte, and the pulling force is measured as a function of DNA extension. In a certain range of spermidine…
Mixtures of polymers of varying topologies and stiffnesses display complex emergent rheological properties that often cannot be predicted from their single-component counterparts. For example, entangled blends of ring and linear polymers…
We present an analytical theory for heteropolymer deformation, as exemplified experimentally by stretching of single protein molecules. Using a mean-field replica theory, we determine phase diagrams for stress-induced unfolding of typical…
Taking into account the nonequivalence of fixed-force and fixed-length ensembles in the weak-force regime, equations of state are derived that describe the equilibrium extension or compression of an ideal Gaussian polymer chain in response…
We propose a theoretical framework for dealing with a transient polymer network undergoing small deformations, based on the rate of breaking and re-forming of network crosslinks and the evolving elastic reference state. In this framework,…
Using Langevin Dynamic simulations, we study effects of the shear force on the rupture of a double stranded DNA molecule. The model studied here contains two single diblock copolymers interacting with each other. The elastic constants of…
We study the enzymatic degradation of an elastic fiber under tension using an an isotropic random-walk model, coupled with binding-unbinding reactions that weaken the fiber. The fiber is represented by a chain of elastic springs in series,…
The chiral nature of DNA plays a crucial role in cellular processes. Here we use magnetic tweezers to explore one of the signatures of this chirality, the coupling between stretch and twist deformations. We show that the extension of a…
Several experiments have demonstrated the existence of an electro-mechanical effect in many biological tissues and hydrogels, and its actual influence on growth, migration, and pattern formation. Here, to model these interactions and…
The non-equilibrium structural and dynamical properties of a flexible polymer tethered to a reflecting wall and subject to oscillatory linear flow are studied by numerical simulations. Polymer is confined in two dimensions and is modeled as…
When quickly detaching an elastomer from a counterface, viscoelasticity dramatically increases the perceived adhesion relative to its adiabatic or equilibrium value. Here, we report simulations on the sticking contact between a rigid…
A simple model of a circularly closed dsDNA in a poor solvent is considered as an example of a semi-flexible polymer with self-attraction. To find the ground states, the conformational energy is computed as a sum of the bending and…
Single molecule DNA experiments often generate data from force versus extension measurements involving the tethering of a microsphere to one end of a single DNA molecule while the other is attached to a substrate. We show that the…
We study the relaxation dynamics of a coarse-grained polymer chain at different degrees of stretching by both analytical means and numerical simulations. The macromolecule is modelled as a string of beads, connected by anharmonic springs,…
In this work, we analyse the stick-slip motion of a soft elastomeric block on a smooth, hard surface under the application of shear, which is induced by a puller moving at a steady velocity. The frictional stress is generated by make-break…
Stretching dynamics of polymers in microfluidics is of particular interest for polymer scientists. As a charged polymer, a polyelectrolyte can be deformed from its coiled equilibrium configuration to an extended chain by applying uniform or…
Using Brownian dynamics simulations, we investigate the dynamics of colloids confined in two-dimensional narrow channels driven by a non-uniform force F(y). We considered linear-gradient, parabolic and delta-like driving-force profiles.…
The spatial organization of DNA involves DNA loop extrusion and the formation of protein-DNA condensates. While the significance of each process is increasingly recognized, their interplay remains unexplored. Using molecular dynamics…
A methodology for the statistical mechanical analysis of polymeric chains under tension introduced previously is extended to include torque. The response of individual bonds between monomers or of entire groups of monomers to a combination…
Polyelectrolytes such as single and double stranded DNA and many synthetic polymers undergo two structural transitions upon increasing the concentration of multivalent salt or molecules. First, the expanded-stretched chains in low…