Chain deformation helps translocation

Abstract

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 electric field inside and outside of a narrow pore is obtained. With an analysis based on "electrohydrodynamic equivalence" we determine the possibility of extension of a charged polymer due to the presence of an electric field gradient in the vicinity of the pore entrance. With a multi-scale hybrid simulation (LB-MD), it is shown that an effective deformation before reaching the pore occurs which facilitates the process of finding the entrance for the end monomers. We also highlight the role of long range hydrodynamic interactions via comparison of the LB-MD results with those obtained using a Langevin thermostat instead of the LB solver.

to appear in softmatter

References in corpus (4)

• The Statistics of DNA Capture by a Solid-State Nanopore
• Thermal fluctuations in the lattice Boltzmann method for non-ideal fluids
• Langevin theory of fluctuations in the discrete Boltzmann equation
• On the importance of hydrodynamic interactions in polyelectrolyte electrophoresis

Cited by in corpus (15)

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• Voltage-Driven Translocation: Defining a Capture Radius
• How capture affects polymer translocation in a solitary nanopore
• Enhanced polymer capture speed and extended translocation time in pressure-solvation traps
• Capture and translocation of a rod-like molecule by a nanopore: orientation, charge distribution and hydrodynamics
• Translocation of short and long polymers through an interacting pore
• An efficient Kinetic Monte Carlo to study analyte capture by a nanopore: Transients, boundary conditions and time-dependent fields
• Dielectric manipulation of polymer translocation dynamics in engineered membrane nanopores
• Ratcheting charged polymers through symmetric nanopores using pulsed fields: Designing a low pass filter for concentrating DNA
• Velocity fluctuation and force scaling during driven polymer transport through a nanopore
• Electrostatics of polymer translocation events in electrolyte solutions
• Polyelectrolytes polarization in non-uniform electric fields