Related papers: DNA electrophoresis in designed channels
We develop an analytical theory that accounts for the image and surface charge interactions between a charged dielectric membrane and a DNA molecule translocating through the membrane. Translocation events through neutral carbon-based…
For single-file translocations of a charged macromolecule through a narrow pore, the crucial step of arrival of an end at the pore suffers from free energy barriers, arising from changes in intrachain electrostatic interaction, distribution…
We present in this paper an original approach to compute the electrophoretic mobility of rigid nucleo-protein complexes like nucleosomes. This model allows to address theoretically the influence of complex position along DNA, as well as…
Deformation of single stranded DNA in translocation process before reaching the pore is investigated. By solving the Laplace equation in a suitable coordinate system and with appropriate boundary conditions, an approximate solution for the…
Nonlinear field dependence of electrophoresis in high fields has been investigated theoretically, yet experimental studies have failed to reach consensus on the effect. In this work, we present a systematic study on the nonlinear…
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…
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…
We present a numerical study of polyelectrolytes electrophoresing in free solution while squeezed by an axisymmetric confinement force transverse to their net displacement. Hybrid multi-particle collision dynamics and molecular dynamics…
Studies of circular DNA confined to nanofluidic channels are relevant both from a fundamental polymer-physics perspective and due to the importance of circular DNA molecules in vivo. We here observe the unfolding of DNA from the circular to…
Electrostatic interactions fundamentally govern the structure and transport of electrolytes. In concentrated electrolytes, however, electrostatic and steric correlations, together with ion-solvent coupling, give rise to complex behavior,…
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…
We investigate the unfolding of single polyelectrolyte (PE) chains collapsed by trivalent salt under the action of alternating-current (AC) electric fields through computer simulations and theoretical scaling. The results show that a…
The present study looks into the pinch-off dynamics of a compound droplet, which is suspended in another fluid in a parallel plate microchannel. The droplet is subjected to a transverse electric field in the presence of an imposed pressure…
We analyse the dynamics of different routes to collapse of a constrained polyelectrolyte gel in contact with an ionic bath. The evolution of the gel is described by a model that incorporates non-linear elasticity, Stefan-Maxwell diffusion…
The control over DNA elongation in nanofluidic devices holds great potential for large-scale genomic analysis. So far, the manipulation of DNA in nanochannels has been mostly carried out with electrophoresis and seldom with hydrodynamics,…
By resorting to a model inspired to the standard Davydov and Holstein-Fr\"ohlich models, in the present paper we study the motion of an electron along a chain of heavy particles modelling a sequence of nucleotides proper to a DNA fragment.…
When electrolyte solutions are confined in micro- and nanochannels their conductivity is significantly different from those in a bulk phase. Here we revisit the theory of this phenomenon by focusing attention on the reduction in the ion…
Gel electrophoresis is a powerful experimental method to probe the topology of DNA and other biopolymers. While there is a large body of experimental work which allows us to accurately separate different topoisomers of a molecule, a full…
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…
We characterize the dynamics of an electrolyte embedded in a varying-section channel under the action of a constant external electrostatic field. By means of molecular dynamics simulations we determine the stationary density, charge and…