Related papers: Dynamics of a double-stranded DNA segment in a she…
The tumbling of a rigid rod in a shear flow is analyzed in the high viscosity limit. Following Burgers, the Master Equation is derived for the probability distribution of the orientation of the rod. The equation contains one dimensionless…
We study the dynamical properties of semiflexible polymers with a recently introduced bead-spring model. We focus on double-stranded DNA. The two parameters of the model, $T^*$ and $\nu$, are chosen to match its experimental force-extension…
To study the elastic properties of rod-like DNA nanostructures, we perform long simulations of these structure using the oxDNA coarse-grained model. By analysing the fluctuations in these trajectories we obtain estimates of the bend and…
The long time behavior of an initial step resulting in a dispersive shock wave (DSW) for the one-dimensional isentropic Euler equations regularized by generic, third order dispersion is considered by use of Whitham averaging. Under modest…
We present a unified scaling description for the dynamics of monomers of a semiflexible chain under good solvent condition in the free draining limit. We consider both the cases where the contour length $L$ is comparable to the persistence…
Entangled polymers are deformed by a strong shear flow. The shape of the polymer, called the form factor, is measured by small angle neutron scattering. However, the real-space molecular structure is not directly available from the…
We present simulations for the steady-shear rheology of a model adhesive dispersion. We vary the range of the attractive forces $u$ as well as the strength of the dissipation $b$. For large dissipative forces, the rheology is governed by…
We study the elastic response of a worm-like polymer chain with reversible kink-like structural defects. This is a generic model for (a) the double-stranded DNA with sharp bends induced by binding of certain proteins, and (b) effects of…
The damping effect to the DNA bubble is investigated within the Peyrard-Bishop model. In the continuum limit, the dynamics of the bubble of DNA is described by the damped nonlinear Schrodinger equation and studied by means of variational…
We give the first correction to the suspension viscosity due to fluid elasticity for a dilute suspension of spheres in a viscoelastic medium. Our perturbation theory is valid to $O(\phi\mathrm{Wi}^2)$ in the Weissenberg number…
In the present work we study the nucleation of Dispersive shock waves (DSW) in the {defocusing}, discrete nonlinear Schr{\"o}dinger equation (DNLS), a model of wide relevance to nonlinear optics and atomic condensates. Here, we study the…
We demonstrate the use of multiscale polymer modelling to quantitatively predict DNA linear dichroism (LD) in shear flow. LD is the difference in absorption of light polarised along two perpendicular axes, and has long been applied to study…
We consider the linearized Euler equations around a smooth, bilipschitz shear profile $U(y)$ on $\mathbb{T}_L \times \mathbb{R}$. We construct an explicit flow which exhibits linear inviscid damping for $L$ sufficiently small, but for which…
We propose that semiflexible polymers in poor solvent collapse in two stages. The first stage is the well known formation of a dense toroidal aggregate. However, if the solvent is sufficiently poor, the condensate will undergo a second…
The dynamics of a stiff filament (made by connecting beads) embedded in size-polydisperse hard sphere fluid is investigated by means of molecular dynamics simulations with focus on how the degree of size-polydispersity, characterized by…
Many structures inside the cell such as nucleosomes and protein-mediated DNA loops contain sharply bent double-stranded (ds) DNA. Therefore, the energetics of strong dsDNA bending constitutes an essential part of cellular thermodynamics.…
The Euler equations on a three-dimensional periodic domain have a family of shear flow steady states. We show that the linearised system around these steady states decomposes into subsystems equivalent to the linearisation of shear flows in…
DNA bending on length scales shorter than a persistence length plays an integral role in the translation of genetic information from DNA to cellular function. Quantitative experimental studies of these biological systems have led to a…
Considering the dynamics of a polymer with finite extensibility placed in a chaotic flow with large mean shear, we explain how the statistics of polymer extension changes with Weissenberg number, ${\it Wi}$, defined as the product of the…
We probe the flow of two dimensional foams, consisting of a monolayer of bubbles sandwiched between a liquid bath and glass plate, as a function of driving rate, packing fraction and degree of disorder. First, we find that bidisperse,…