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Register a new userUnexpected relaxation dynamics of a self-avoiding polymer in cylindrical confinement
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We report extensive simulations of the relaxation dynamics of a self-avoiding polymer confined inside a cylindrical pore. In particular, we concentrate on examining how confinement influences the scaling behavior of the global relaxation time of the chain, t, with the chain length N and pore diameter D. An earlier scaling analysis based on the de Gennes blob picture led to t ~ N^2D^(1/3). Our numerical effort that combines molecular dynamics and Monte Carlo simulations, however, consistently produces different t-results for N up to 2000. We argue that the previous scaling prediction is only asymptotically valid in the limit N >> D^(5/3) >> 1, which is currently inaccessible to computer simulations and, more interestingly, is also difficult to reach in experiments. Our results are thus relevant for the interpretation of recent experiments with DNA in nano- and micro-channels.
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Using Langevin dynamics simulations, we investigate the dynamics of a flexible polymer translocation into a confined area under a driving force through a nanopore. We choose an ellipsoidal shape for the confinement and consider the dependence of the asymmetry of the ellipsoid measured by the aspect ratio on the translocation time. Compared with an isotropic confinement (sphere), an anisotropic confinement (ellipsoid) with the same volume slows down the translocation, and the translocation time increases with increasing the aspect ratio of the ellipsoid. We further find that it takes different time for polymer translocation into the same ellipsoid through major-axis and minor-axis directions, depending on the average density of the whole chain in the ellipsoid, $phi$. For $phi$ lower than a critical value $phi_c$, the translocation through minor axis is faster, and vice versa. These complicated behaviors are interpreted by the degree of the confinement and anisotropic confinement induced folding of the translocated chain.
We investigate by means of molecular dynamics simulation a coarse-grained polymer glass model focusing on (quasi-static and dynamical) shear-stress fluctuations as a function of temperature T and sampling time $Delta t$. The linear response is characterized using (ensemble-averaged) expectation values of the contributions (time-averaged for each shear plane) to the stress-fluctuation relation $mu_{sf}$ for the shear modulus and the shear-stress relaxation modulus $G(t)$. Using 100 independent configurations we pay attention to the respective standard deviations. While the ensemble-averaged modulus $mu_{sf}(T)$ decreases continuously with increasing T for all $Delta t$ sampled, its standard deviation $delta mu_{sf}(T)$ is non-monotonous with a striking peak at the glass transition. The question of whether the shear modulus is continuous or has a jump-singularity at the glass transition is thus ill-posed. Confirming the effective time-translational invariance of our systems, the $Delta t$-dependence of $mu_{sf}$ and related quantities can be understood using a weighted integral over $G(t)$. This implies that the shear viscosity $eta(T)$ may be readily obtained from the $1/Delta t$-decay of $mu_{sf}$ above the glass transition.
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.
We perform numerical simulations of an active fully flexible self-avoiding polymer as a function of the quality of the embedding solvent described in terms of an effective monomer-monomer interaction. Specifically, by extracting the Flory exponent of the active polymer under different conditions, we are able to pin down the location of the coil-globule transition for different strength of the active forces. Remarkably, we find that a simple rescaling of the temperature is capable of qualitatively capture the dependence of the $Theta$-point of the polymer with the amplitude of the active fluctuations. We discuss the limits of this mapping, and suggest that a negative active pressure between the monomers, not unlike the one that has already been found in suspensions of active hard spheres, may also be present in active polymers.
Molecular Dynamics simulations of a coarse-grained bead-spring model of flexible macromolecules tethered with one end to the surface of a cylindrical pore are presented. Chain length $N$ and grafting density $sigma$ are varied over a wide range and the crossover from ``mushroom to ``brush behavior is studied for three pore diameters. The monomer density profile and the distribution of the free chain ends are computed and compared to the corresponding model of polymer brushes at flat substrates. It is found that there exists a regime of $N$ and $sigma$ for large enough pore diameter where the brush height in the pore exceeds the brush height on the flat substrate, while for large enough $N$ and $sigma$ (and small enough pore diameters) the opposite behavior occurs, i.e. the brush is compressed by confinement. These findings are used to discuss the corresponding theories on polymer brushes at concave substrates.
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