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Register a new userPolymer Escape from a Metastable Kramers potential: Path Integral Hyperdynamics Study
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We study the dynamics of flexible, semiflexible, and self-avoiding polymer chains moving under a Kramers metastable potential. Due to thermal noise, the polymers, initially placed in the metastable well, can cross the potential barrier, but these events are extremely rare if the barrier is much larger than thermal energy. To speed up the slow rate processes in computer simulations, we extend the recently proposed path integral hyperdynamics method to the cases of polymers. We consider the cases where the polymers radii of gyration are comparable to the distance between the well bottom and the barrier top. We find that, for a flexible polymer, the crossing rate ($mathcal{R}$) monotonically decreases with chain contour length ($L$), but with the magnitude much larger than the Kramers rate in the globular limit. For a semiflexible polymer, the crossing rate decreases with $L$ but becomes nearly constant for large $L$. For a fixed $L$, the crossing rate becomes maximum at an intermediate bending stiffness. For a self-avoiding chain, the rate is a nonmonotonic function of $L$, first decreasing with $L$, and then, above certain length, increasing with $L$. These findings can be instrumental for efficient separation of biopolymers.
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A correlation between two noise processes driving the thermally activated particles in a symmetric triple well potential, may cause a symmetry breaking and a difference in relative stability of the two side wells with respect to the middle one. This leads to an asymmetric localization of population and splitting of Kramers rate of escape from the middle well, ensuring a preferential distribution of the products in the course of a parallel reaction.
We study conformations of the Gaussian polymer chains in d-dimensional space in the presence of an external field with the harmonic potential. We apply a path integral approach to derive an explicit expression for the probability distribution function of the gyration radius. We calculate this function using Monte Carlo simulations and show that our numerical and theoretical results are in a good agreement for different values of the external field.
We study escape dynamics of a double-stranded DNA (dsDNA) through an idealized double nanopore (DNP) geometry subject to two equal and opposite forces (tug-of-war) using Brownian dynamics (BD) simulation. In addition to the geometrical restrictions imposed on the cocaptured dsDNA segment in between the pores, the presence of tug-of-war forces at each pore results in a variation of the local chain stiffness for the segment of the chain in between the pores which increases the overall stiffness of the chain. We use BD simulation results to understand how the intrinsic chain stiffness and the TOW forces affect the escape dynamics by monitoring the local chain persistence length $ell_p$, the residence time of the individual monomers $W(m)$ in the nanopores, and the chain length dependence of the escape time $langle tau rangle$ and its distribution. Finally, we generalize the scaling theory for the unbiased single nanopore translocation for a fully flexible chain for the escape of a semi-flexible chain through a DNP in presence of TOW forces. We establish that the stiffness dependent part of the escape time is approximately independent of the translocation mechanism so that $langle tau rangle sim ell_p^{2/D+2}$, and therefore the generalized escape time for a semi-flexible chain can be written as $langle tau rangle = AN^alphaell_p^{2/D+2}$. We use BD simulation results to compare the predictions of the scaling theory. Our numerical studies supplemented by scaling analysis provide fundamental insights to design new experiments where a dsDNA moves slowly through a series of graphene nanopores.
DNA renaturation is the recombination of two complementary single strands to form a double helix. It is experimentally known that renaturation proceeds through the formation of a double stranded nucleus of several base pairs (the rate limiting step) followed by a much faster zippering. We consider a lattice polymer model undergoing Rouse dynamics and focus on the nucleation of two diffusing strands. We study numerically the dependence of various nucleation rates on the strand lengths and on an additional local nucleation barrier. When the local barrier is sufficiently high, all renaturation rates considered scale with the length as predicted by Kramers rate theory and are also in agreement with experiments: their scaling behavior is governed by exponents describing equilibrium properties of polymers. When the local barrier is lowered renaturation occurs in a regime of genuine non-equilibrium behavior and the scaling deviates from the rate theory prediction.
The escape transition of a polymer mushroom (a flexible chain grafted to a flat non-adsorbing substrate surface in a good solvent) occurs when the polymer is compressed by a cylindrical piston of radius $R$, that by far exceeds the chain gyration radius. At this transition, the chain conformation abruptly changes from a two-dimensional self-avoiding walk of blobs (of diameter $H$, the height of the piston above the substrate) to a flower conformation, i.e. stretched almost one-dimensional string of blobs (with end-to-end distance $approx R$) and an escaped part of the chain, the crown, outside the piston. The extension of this problem to the case of star polymers with $f$ arms is considered, assuming that the center of the star is grafted to the substrate. The question is considered whether under compression the arms escape all together, or whether there occurs an arm by arm escape under increasing compression. Both self-consistent field calculations and Molecular Dynamics simulations are found to favor the latter scenario.
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