Related papers: Dynamics of a double-stranded DNA segment in a she…
The steady-state behavior of a dilute suspension of self-propelled filaments confined between planar walls subjected to the Couette-flow is reported herein. The effect of hydrodynamics has been taken into account using a mesoscale…
Polymer melts with chains undergoing reversible crosslinking have distinctively favorable dynamic properties, e.g., self healing and reprocessability. In these situations there are two relevant elementary time scales: the segmental and the…
Using non-equilibrium Brownian dynamics computer simulations, we have investigated the steady state statistics of a polymer chain under three different shear environments: i) linear shear flow in the bulk (no walls), ii) shear vorticity…
We examine how perturbed shear flows evolve in two-dimensional, incompressible, inviscid hydrodynamical fluids, with the ultimate goal of understanding the dynamics of accretion disks. To linear order, vorticity waves are swung around by…
The mechanical properties of molecules are today captured by single molecule manipulation experiments, so that polymer features are tested at a nanometric scale. Yet devising mathematical models to get further insight beyond the commonly…
The closure dynamics of a pre-equilibrated DNA denaturation bubble is studied using both Brownian dynamics simulations and an analytical approach. The numerical model consists of two semi-flexible interacting single strands (ssDNA) 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)…
The mechanical properties of a polymeric network containing both crosslinks and sliplinks (entanglements) are studied using a multi-chain Brownian dynamics simulation. We coarse-grain at the level of chain segments connecting consecutive…
We show theoretically that an initially homogeneous planar Couette flow of a concentrated polymeric fluid is linearly unstable to the growth of two-dimensional (2D) perturbations, within two widely used constitutive models: the…
Blends of polymers of different topologies, such as ring and supercoiled, naturally occur in biology and often exhibit emergent viscoelastic properties coveted in industry. However, due to their complexity, along with the difficulty of…
The effects induced by long temporal correlations of the velocity gradients on the dynamics of a flexible polymer are investigated by means of theoretical and numerical analysis of the Hookean and FENE dumbbell models in a random renewing…
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 self-excited spanwise homogeneous perturbations arising in shock-wave/boundary-layer interaction (SWBLI) system formed in a hypersonic flow of molecular nitrogen over a double wedge are investigated using the kinetic Direct Simulation…
A detailed description of the conformational plasticity of double stranded DNA (ds) is a necessary framework for understanding protein-DNA interactions. Until now, however structure and kinetics of the transition from the basic conformation…
The intricate wobbling motion of flagellated bacteria, characterized by the periodic precession of the cell body, is a determinant factor in their motility and navigation within complex fluid environments. While well-studied in quiescent…
We present a theoretical study of single-stranded DNA under stretching. Within the proposed framework, the effects of basepairing on the mechanical response of the molecule can be studied in combination with an arbitrary underlying model of…
We study the influence of chain stiffness on droplet flow in a nano-channel, coated with semiflexible hydrophobic polymers by means of non-equilibrium molecular-dynamics simulations. The studied system is then a moving droplet in the slit…
We study a class of micromanipulation experiments, exemplified by the pulling apart of the two strands of double-stranded DNA (dsDNA). When the pulling force is increased to a critical value, an ``unzipping'' transition occurs. For random…
Bead spring models for polymers in solution are nonlinear if either the finite extensibility of the polymer, excluded volume effects or hydrodynamic interactions between polymer segments are taken into account. For such models we use a…
Although the non-equilibrium behaviour of polymer solutions is generally well understood, particularly in extensional flow, there remain several unanswered questions for dilute solutions in simple shear flow, and full quantitative agreement…