September 15, 2005
We present a simple description on the electrophoretic dynamics of polyelectrolytes going through designed channels with narrow constrictions of slit geometry. By analyzing rheological behaviours of the stuck chain, which is coupled to the effect of solvent flow, three critical electric fields (permeation field $E^{(per)} \sim N^{-1}$, deformation field $E^{(def)} \sim N^{-3/5}$ and injection field $E^{(inj)} \simeq N^0$, with $N$ polymerization index) are clarified. Between $E^{(per)}$ and $E^{(inj)}$, the chain migration is dictated by the driven activation process. In particular, at $E>E^{(def)}$, the stuck chain at the slit entrance is strongly deformed, which enhances the rate of the permeation. From these observations, electrophoretic mobility at a given electric field is deduced, which shows non-monotonic dependence on $N$. For long enough chains, mobility increases with $N$, in good agreement with experiments. An abrupt change in the electrophoretic flow at a threshold electric field is formally regarded as a nonequilibrium phase transition.
Similar papers 1
July 18, 2006
We study migration of DNA molecules through a microchannel with a series of electric traps controlled by an ac electric field. We describe the motion of DNA based on Brownian dynamics simulations of a beads-spring chain. Our simulation demonstrates that the chain captured by an electrode escapes from the binding electric field due to thermal fluctuation. We find that the mobility of chain would depend on the chain length; the mobility sharply increases when the length of a ch...
June 19, 2013
Motivated by DNA electrophoresis near a nanopore, we consider the flow field around an "elongated jet", a long thin source which injects momentum into a liquid. This solution qualitatively describes the electro-osmotic flow around a long rigid polymer, where due to electrohydrodynamic coupling, the solvent receives momentum from the electric field. Based on the qualitative behavior of the elongated jet solution, we develop a coarse-grained scheme which reproduces the known th...
September 28, 2006
A hydrodynamic model for determining the electrophoretic speed of a polyelectrolyte through a nanopore is presented. It is assumed that the speed is determined by a balance of electrical and viscous forces arising from within the pore and that classical continuum electrostatics and hydrodynamics may be considered applicable. An explicit formula for the translocation speed as a function of the pore geometry and other physical parameters is obtained and is shown to be consisten...
February 17, 1999
Motivated by experiments in which a polynucleotide is driven through a proteinaceous pore by an electric field, we study the diffusive motion of a polymer threaded through a narrow channel with which it may have strong interactions. We show that there is a range of polymer lengths in which the system is approximately translationally invariant, and we develop a coarse-grained description of this regime. From this description, general features of the distribution of times for t...
January 6, 2010
We present mesoscopic DPD-simulations of polyelectrolyte electrophoresis in confined nanogeometries, for varying salt concentration and surface slip conditions. Special attention is given to the influence of electroosmotic flow (EOF) on the migration of the polyelectrolyte. The effective polyelectrolyte mobility is found to depend strongly on the boundary properties, i.e., the slip length and the width of the electric double layer. Analytic expressions for the electroosmotic ...
February 25, 2012
The electric-field-driven entry process of flexible charged polymers such as single stranded DNA (ssDNA) into asymmetric nanoscale channels such as alpha-hemolysin protein channel is studied theoretically and using molecular dynamics simulations. Dependence of the height of the free-energy barrier on the polymer length, the strength of the applied electric field and the channel entrance geometry is investigated. It is shown that the squeezing effect of the driving field on th...
June 19, 2013
Based on our formulation of the DNA electrophoresis near a pore [P. Rowghanian and A. Y. Grosberg, Phys. Rev. E 87, 042723 (2013)], we address the electrophoretic DNA capture into a nanopore as a steady-state process of particle absorption to a sink placed on top of an energy barrier. Reproducing the previously observed diffusion-limited and barrier-limited regimes as two different limits of the particle absorption process and matching the data, our model suggests a slower gr...
March 20, 2005
We propose a new method for electrophoretic separation of DNA in which adsorbed polymers are driven over a disordered two-dimensional substrate which contains attractive sites for the polymers. Using simulations of a model for long polymer chains, we show that the mobility increases with polymer length, in contrast to gel electrophoresis techniques, and that separation can be achieved for a range of length scales. We demonstrate that the separation mechanism relies on steric ...
September 11, 2020
The transport of polyelectrolytes confined by oppositely charged surfaces and driven by a constant electric field is of interest in studies of DNA separation according to size. Using molecular dynamics simulations that include surface polarization effect, we find that the mobilities of the polyelectrolytes and their counterions change non-monotonically with the confinement surface charge density. For an optimum value of the confinement charge density, efficient separation of ...
July 16, 2019
We consider the influence of electrostatic forces on driven translocation dynamics of a flexible polyelectrolyte being pulled through a nanopore by an external force on the head monomer. To this end, we augment the iso-flux tension propagation (IFTP) theory with electrostatics for a negatively charged biopolymer pulled through a nanopore embedded in a similarly charged anionic membrane. We show that for the realistic case such as a single-stranded DNA, the translocation dynam...