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Register a new userA string reaction coordinate for the folding of a polymer chain
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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.
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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.
Using analytical techniques and Langevin dynamics simulations, we investigate the dynamics of polymer translocation into a narrow channel of width $R$ embedded in two dimensions, driven by a force proportional to the number of monomers in the channel. Such a setup mimics typical experimental situations in nano/micro-fluidics. During the the translocation process if the monomers in the channel can sufficiently quickly assume steady state motion, we observe the scaling $tausim N/F$ of the translocation time $tau$ with the driving force $F$ per bead and the number $N$ of monomers per chain. With smaller channel width $R$, steady state motion cannot be achieved, effecting a non-universal dependence of $tau$ on $N$ and $F$. From the simulations we also deduce the waiting time distributions under various conditions for the single segment passage through the channel entrance. For different chain lengths but the same driving force, the curves of the waiting time as a function of the translocation coordinate $s$ feature a maximum located at identical $s_{mathrm{max}}$, while with increasing the driving force or the channel width the value of $s_{mathrm{max}}$ decreases.
We examine the phase transition of polymer adsorption as well as the underlying kinetics of polymer binding from dilute solutions on a structureless solid surface. The emphasis is put on the properties of regular multiblock copolymers, characterized by block size M and total length N as well as on random copolymers with quenched composition p of sticky and neutral segments. The macromolecules are modeled as coarse-grained bead-spring chains subject to a short-ranged surface adhesive potential. Phase diagrams, showing the variation of the critical threshold for single chain adsorption in terms of M and p are derived from scaling considerations in agreement with results from computer experiment. Using both scaling analysis and numerical data from solving a system of coupled Master equations, we demonstrate that the phase behavior at criticality, and the adsorption kinetics may be adequately predicted and understood, in agreement with the results of extensive Monte Carlo simulations. Derived analytic expressions for the mean fraction of adsorbed segments as well as for Probability Distribution Functions of the various structural building blocks (i.e., trains, loops, tails) at time t during the chain attachment process are in good agreement with our numeric experiments and provide insight into the mechanism of polymer adsorption.
Using analytical techniques and Langevin dynamics simulations, we investigate the dynamics of polymer translocation through a nanochannel embedded in two dimensions under an applied external field. We examine the translocation time for various ratio of the channel length $L$ to the polymer length $N$. For short channels $Lll N$, the translocation time $tau sim N^{1+ u}$ under weak driving force $F$, while $tausim F^{-1}L$ for long channels $Lgg N$, independent of the chain length $N$. Moreover, we observe a minimum of translocation time as a function of $L/N$ for different driving forces and channel widths. These results are interpreted by the waiting time of a single segment.
We propose a lattice model for RNA based on a self-interacting two-tolerant trail. Self-avoidance and elements of tertiary structure are taken into account. We investigate a simple version of the model in which the native state of RNA consists of just one hairpin. Using exact arguments and Monte Carlo simulations we determine the phase diagram for this case. We show that the denaturation transition is first order and can either occur directly or through an intermediate molten phase.
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