Related papers: Dynamics of a double-stranded DNA segment in a she…
The extensional rheology of polymeric liquids has been extensively examined through experiments and theoretical predictions. However, a systematic study of the extensional rheology of polymer solutions in the semidilute regime, in terms of…
The structure and vibrational density of states (VDOS) of polymer glasses are investigated using numerical simulations based on the classical Kremer-Grest bead-spring model. We focus on the roles of chain length and bending stiffness, the…
Simple expressions for the bending and the base-stacking energy of double-stranded semiflexible biopolymers (such as DNA and actin) are derived. The distribution of the folding angle between the two strands is obtained by solving a…
Single molecule experiments on B-DNA stretching have revealed one or two structural transitions, when increasing the external force. They are characterized by a sudden increase of DNA contour length and a decrease of the bending rigidity.…
A double stranded DNA molecule under the stress of a pulling force acting on the strand terminals exhibits a partially denatured structure or can be completely unzipped depending the magnitude of the pulling force. A scaling argument for…
Using molecular dynamics simulations, we study dynamics of a model polymer melt composed of short chains with bead number N=10 in supercooled states. In quiescent conditions, the stress relaxation function $G(t)$ is calculated, which…
Double-stranded DNA `overstretches' at a pulling force of about 65 pN, increasing in length by a factor of 1.7. The nature of the overstretched state is unknown, despite its considerable importance for DNA's biological function and…
The Peierls instability, the spontaneous dimerization of a one-dimensional metallic chain at half filling, is a paradigmatic mechanism for charge-density-wave (CDW) formation. Here we test its robustness under finite doping and interchain…
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 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…
Biological membranes are host to proteins and molecules which may form domain-like structures resulting in spatially-varying material properties. Vesicles with such heterogeneous membranes can exhibit intricate shapes at equilibrium and…
DNA toroids are compact torus-shaped bundles formed by one or multiple DNA molecules being condensed from the solution due to various condensing agents. It has been shown that the DNA toroidal bundles are twisted. However, the global…
We present experiments on the dynamic buckling and fragmentation of slender rods axially impacted by a projectile. By combining the results of Saint-Venant and elastic beam theory, we derive a preferred wavelength lambda for the buckling…
We investigate previously unclarified effects of fluid elasticity on shear-thickening in dilute suspensions in an Oldroyd-B viscoelastic fluid using a novel direct numerical simulation based on the smoothed profile method. Fluid elasticity…
A simple model of DNA based on two interacting polymers has been used to study the unzipping of a double stranded DNA subjected to a periodic force. We propose a dynamical transition, where without changing the physiological condition, it…
We present a time-dependent Ginzburg-Landau model of nonlinear elasticity in solid materials. We assume that the elastic energy density is a periodic function of the shear and tetragonal strains owing to the underlying lattice structure.…
A time-dependent Ginzburg-Landau model of plastic deformation in two-dimensional solids is presented. The fundamental dynamic variables are the displacement field $\bi u$ and the lattice velocity ${\bi v}=\p {\bi u}/\p t$. Damping is…
We investigate the nonlinear dynamics of a damped Peyrard-Bishop DNA model taking into account long-range interactions with distance dependence |l|^-s on the elastic coupling constant between different DNA base pairs. Considering both…
The dynamics of fluid vesicles in simple shear flow is studied using mesoscale simulations of dynamically-triangulated surfaces, as well as a theoretical approach based on two variables, a shape parameter and the inclination angle, which…
The dynamics of polymers in a random smooth flow is investigated in the framework of the Hookean dumbbell model. The analytical expression of the time-dependent probability density function of polymer elongation is derived explicitly for a…