Force-driven translocation of a macromolecule through a nanopore is investigated by taking into account the monomer-pore friction as well as the crowding of monomers on the {it trans} - side of the membrane which counterbalance the driving force acti
ng in the pore. The set of governing differential-algebraic equations for the translocation dynamics is derived and solved numerically. The analysis of this solution shows that the crowding of monomers on the trans side hardly affects the dynamics, but the monomer-pore friction can substantially slow down the translocation process. Moreover, the translocation exponent $alpha$ in the translocation time - vs. - chain length scaling law, $tau propto N^{alpha}$, becomes smaller when monomer-pore friction coefficient increases. This is most noticeable for relatively strong forces. Our findings may explain the variety of $alpha$ values which were found in experiments and computer simulations.
Forced detachment of a single polymer chain, strongly-adsorbed on a solid substrate, is investigated by two complementary methods: a coarse-grained analytical dynamical model, based on the Onsager stochastic equation, and Molecular Dynamics (MD) simu
lations with Langevin thermostat. The suggested approach makes it possible to go beyond the limitations of the conventional Bell-Evans model. We observe a series of characteristic force spikes when the pulling force is measured against the cantilever displacement during detachment at constant velocity $v_c$ (displacement control mode) and find that the average magnitude of this force increases as $v_c$ grows. The probability distributions of the pulling force and the end-monomer distance from the surface at the moment of final detachment are investigated for different adsorption energy $epsilon$ and pulling velocity $v_c$. Our extensive MD-simulations validate and support the main theoretical findings. Moreover, the simulation reveals a novel behavior: for a strong-friction and massive cantilever the force spikes pattern is smeared out at large $v_c$. As a challenging task for experimental bio-polymers sequencing in future we suggest the fabrication of stiff, super-light, nanometer-sized AFM probe.
We analyze the dynamics of desorption of a polymer molecule which is pulled at one of its ends with force $f$, trying to desorb it. We assume a monomer to desorb when the pulling force on it exceeds a critical value $f_{c}$. We formulate an equation
for the average position of the $n^{th}$ monomer, which takes into account excluded volume interaction through the blob-picture of a polymer under external constraints. The approach leads to a diffusion equation with a $p$-Laplacian for the propagation of the stretching along the chain. This has to be solved subject to a moving boundary condition. Interestingly, within this approach, the problem can be solved exactly in the trumpet, stem-flower and stem regimes. In the trumpet regime, we get $tau=tau_{0}n_d^{2}$ where $n_d$ is the number of monomers that have desorbed at the time $tau$. $tau_{0}$ is known only numerically, but for $f$ close to $f_{c}$, it is found to be $tau_{0}sim f_c/(f^{2/3}-f_{c}^{2/3})$. If one used simple Rouse dynamics, this result changes to { ormalsize $tausim f_c n_d^2/(f-f_{c})$.} In the other regimes too, one can find exact solution, and interestingly, in all regimes $tau sim n_d^2$.
The breakage of a polymer chain of segments, coupled by anharmonic bonds with applied constant external tensile force is studied by means of Molecular Dynamics simulation. We show that the mean life time of the chain becomes progressively independent
of the number of bonds as the pulling force grows. The latter affects also the rupture rates of individual bonds along the polymer backbone manifesting the essential role of inertial effects in the fragmentation process. The role of local defects, temperature and friction in the scission kinetics is also examined.
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 fl
uctuating 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 study analytically and by means of an off-lattice bead-spring dynamic Monte Carlo simulation model the adsorption kinetics of a single macromolecule on a structureless flat substrate in the regime of strong physisorption. The underlying notion of
a ``stem-flower polymer conformation, and the related mechanism of ``zipping during the adsorption process are shown to lead to a Fokker-Planck equation with reflecting boundary conditions for the time-dependent probability distribution function (PDF) of the number of adsorbed monomers. The theoretical treatment predicts that the mean fraction of adsorbed segments grows with time as a power law with a power of $(1+ u)^{-1}$ where $ uapprox 3/5$ is the Flory exponent. The instantaneous distribution of train lengths is predicted to follow an exponential relationship. The corresponding PDFs for loops and tails are also derived. The complete solution for the time-dependent PDF of the number of adsorbed monomers is obtained numerically from the set of discrete coupled differential equations and shown to be in perfect agreement with the Monte Carlo simulation results. In addition to homopolymer adsorption, we study also regular multiblock copolymers and random copolymers, and demonstrate that their adsorption kinetics may be considered within the same theoretical model.
