The impact of thermal fluctuations on the translocation dynamics of a polymer chain driven through a narrow pore has been investigated theoretically and by means of extensive Molecular-Dynamics (MD) simulation. The theoretical consideration is based
on the so-called velocity Langevin (V-Langevin) equation which determines the progress of the translocation in terms of the number of polymer segments, $s(t)$, that have passed through the pore at time $t$ due to a driving force $f$. The formalism is based only on the assumption that, due to thermal fluctuations, the translocation velocity $v=dot{s}(t)$ is a Gaussian random process as suggested by our MD data. With this in mind we have derived the corresponding Fokker-Planck equation (FPE) which has a nonlinear drift term and diffusion term with a {em time-dependent} diffusion coefficient $D(t)$. Our MD simulation reveals that the driven translocation process follows a {em super}diffusive law with a running diffusion coefficient $D(t) propto t^{gamma}$ where $gamma < 1$. This finding is then used in the numerical solution of the FPE which yields an important result: for comparatively small driving forces fluctuations facilitate the translocation dynamics. As a consequence, the exponent $alpha$ which describes the scaling of the mean translocation time $<tau>$ with the length $N$ of the polymer, $<tau> propto N^{alpha}$ is found to diminish. Thus, taking thermal fluctuations into account, one can explain the systematic discrepancy between theoretically predicted duration of a driven translocation process, considered usually as a deterministic event, and measurements in computer simulations. In the non-driven case, $f=0$, the translocation is slightly subdiffusive and can be treated within the framework of fractional Brownian motion (fBm).
The force-assisted desorption kinetics of a macromolecule from adhesive surface is studied theoretically, using the notion of tensile (Pincus) blobs, as well as by means of Monte-Carlo (MC) and Molecular Dynamics (MD) simulations. We show that the ch
ange of detached monomers with time is governed by a differential equation which is equivalent to the nonlinear porous medium equation (PME), employed widely in transport modeling of hydrogeological systems. Depending on the pulling force and the strength of adsorption, three kinetic regimes can be distinguished: (i) trumpet (weak adsorption and small pulling force), (ii) stem-trumpet (weak adsorption and moderate force), and (iii) stem (strong adsorption and large force). Interestingly, in all regimes the number of desorbed beads $M(t)$, and the height of the first monomer (which experiences a pulling force) $R(t)$ above the surface follow an universal square-root-of-time law. Consequently, the total time of detachment $<tau_d>$, scales with polymer length $N$ as $<tau_d> propto N^2$. Our main theoretical conclusions are tested and found in agreement with data from extensive MC- and MD-simulations.
We suggest a theoretical description of the force-induced translocation dynamics of a polymer chain through a nanopore. Our consideration is based on the tensile (Pincus) blob picture of a pulled chain and the notion of propagating front of tensile f
orce along the chain backbone, suggested recently by T. Sakaue. The driving force is associated with a chemical potential gradient that acts on each chain segment inside the pore. Depending on its strength, different regimes of polymer motion (named after the typical chain conformation, trumpet, stem-trumpet, etc.) occur. Assuming that the local driving and drag forces are equal (i.e., in a quasi-static approximation), we derive an equation of motion for the tensile front position $X(t)$. We show that the scaling law for the average translocation time $<tau>$ changes from $<tau> sim N^{2 u}/f^{1/ u}$ to $<tau> sim N^{1+ u}/f$ (for the free-draining case) as the dimensionless force ${widetilde f}_{R} = a N^{ u}f /T$ (where $a$, $N$, $ u$, $f$, $T$ are the Kuhn segment length, the chain length, the Flory exponent, the driving force, and the temperature, respectively) increases. These and other predictions are tested by Molecular Dynamics (MD) simulation. Data from our computer experiment indicates indeed that the translocation scaling exponent $alpha$ grows with the pulling force ${widetilde f}_{R}$) albeit the observed exponent $alpha$ stays systematically smaller than the theoretically predicted value. This might be associated with fluctuations which are neglected in the quasi-static approximation.
We show that the structural properties and phase behavior of a self-avoiding polymer chain on adhesive substrate, subject to pulling at the chain end, can be obtained by means of a Grand Canonical Ensemble (GCE) approach. We derive analytical express
ions for the mean length of the basic structural units of adsorbed polymer, such as loops and tails, in terms of the adhesive potential and detachment force, and determine values of the universal exponents which govern their probability distributions. Most notably, the hitherto controversial value of the critical adsorption exponent $phi$ is found to depend essentially on the interaction between different loops. The chain detachment transition turns out to be of the first order, albeit dichotomic, i.e., no coexistence of different phase states exists. These novel theoretical predictions and the suggested phase diagram of the adsorption-desorption transformation under external pulling force are verified by means of extensive Monte Carlo simulations.
