Tethered polymers in a shear flow: A molecular dynamics study of the good and bad solvent cases
Nanotechnology is now a reality although it is still very much in its infancy. This being said much work still needs to be done. During the last past few decades, new experimental tools such as videomicroscopy and optical tweezers, which allow us to both visualize and manipulate in real time the dynamics of macromolecules, have emerged. These two tools alone provide endless possibilities. For example, it is now possible to tether a polymer at one end with optical tweezers while a constant flow
... f solvent extends it. If the chain is fluorescently labeled, dynamical properties can be extracted via videomicroscopy. In this thesis, we study a similar problem. With the help of Molecular Dynamics (MD) simulations, we examine the physics of a Freely Jointed Chain (FJC) tethered by one end to a hard surface while being submitted to a Poiseuille flow. A good solvent is used during the first part of this thesis, while for the second part, we look at the dynamics of the chain in poor solvents. In both cases, we compare actual stretching theories to our simulation data and extract the effects of Hydrodynamic Interactions (HI). For good solvents, we propose a new empirical equation which relates the unstretched fraction of the chain to the full range of shear rates. We also observe a peculiar cyclic motion of the chain which was first reported experimentally. For poor solvents, we study the collapsed chain properties while changing the strength of the shear flow linearly in time. A novel hysteretic effect for the chain extension as a function of shear rate is observed in our simulations.