No Arabic abstract
We extend the Rouse model of polymer dynamics to situations of non-stationary chain growth. For a dragged polymer chain of length $N(t) = t^alpha$, we find two transitions in conformational dynamics. At $alpha= 1/2$, the propagation of tension and the average shape of the chain change qualitatively, while at $alpha = 1 $ the average center-of-mass motion stops. These transitions are due to a simple physical mechanism: a race duel between tension propagation and polymer growth. Therefore they should also appear for growing semi-flexible or stiff polymers. The generalized Rouse model inherits much of the versatility of the original Rouse model: it can be efficiently simulated and it is amenable to analytical treatment.
We present micro-rheological measurments of the drag force on colloids pulled through a solution of lambda-DNA (used here as a monodisperse model polymer) with an optical tweezer. The experiments show a violation of the Stokes-Einstein relation based on the independently measured viscosity of the DNA solution: the drag force is larger than expected. We attribute this to the accumulation of DNA infront of the colloid and the reduced DNA density behind the colloid. This hypothesis is corroborated by a simple drift-diffusion model for the DNA molecules, which reproduces the experimental data surprisingly well, as well as by corresponding Brownian dynamics simulations.
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, subject to a tensile force applied at the end monomer of the chain while the other end is fixed at the origin of coordinates. The impact of bond non-linearity on the relaxation dynamics of the polymer at different degrees of stretching is treated analytically within the Gaussian self-consistent approach (GSC) and then compared to simulation results derived from two different methods: Monte-Carlo (MC) and Molecular Dynamics (MD). At low and medium degrees of chain elongation we find good agreement between GSC predictions and the Monte-Carlo simulations. However, for strongly stretched chains the MD method, which takes into account inertial effects, reveals two important aspects of the nonlinear interaction between monomers: (i) a coupling and energy transfer between the damped, oscillatory normal modes of the chain, and (ii) the appearance of non-vanishing contributions of a continuum of frequencies around the characteristic modes in the power spectrum of the normal mode correlation functions.
The thermally assisted detachment of a self-avoiding polymer chain from an adhesive surface by an external force applied to one of the chain ends is investigated. We perform our study in the fixed height statistical ensemble where one measures the fluctuating force, exerted by the chain on the last monomer when a chain end is kept fixed at height $h$ over the solid plane at different adsorption strength $epsilon$. The phase diagram in the $h - epsilon$ plane is calculated both analytically and by Monte Carlo simulations. We demonstrate that in the vicinity of the polymer desorption transition a number of properties like fluctuations and probability distribution of various quantities behave differently, if $h$ rather than $f$ is used as an independent control parameter.
We investigate the crystallization mechanism of a single, flexible homopolymer chain with short range attractions. For a sufficiently narrow attractive well, the system undergoes a first-order like freezing transition from an expanded disordered coil to a compact crystalline state. Based on a maximum likelihood analysis of committor values computed for configurations obtained by Wang-Landau sampling, we construct a non-linear string reaction coordinate for the coil-to-crystal transition. In contrast to a linear reaction coordinate, the string reaction coordinate captures the effect of different degrees of freedom controlling different stages of the transition. Our analysis indicates that a combination of the energy and the global crystallinity parameter Q6 provide the most accurate measure for the progress of the transition. While the crystallinity parameter Q6 is most relevant in the initial stages of the crystallization, the later stages are dominated by a decrease in the potential energy.
We determine the scaling exponents of polymer translocation (PT) through a nanopore by extensive computer simulations of various microscopic models for chain lengths extending up to N=800 in some cases. We focus on the scaling of the average PT time $tau sim N^{alpha}$ and the mean-square change of the PT coordinate $<s^2(t)> sim t^beta$. We find $alpha=1+2 u$ and $beta=2/alpha$ for unbiased PT in 2D and 3D. The relation $alpha beta=2$ holds for driven PT in 2D, with crossover from $alpha approx 2 u$ for short chains to $alpha approx 1+ u$ for long chains. This crossover is, however, absent in 3D where $alpha = 1.42 pm 0.01$ and $alpha beta approx 2.2$ for $N approx 40-800$.