Modeling the current modulation of dsDNA in nanopores – from mean-field to atomistic and back

All-atom molecular dynamics (MD) simulations of double stranded DNA (dsDNA) translocating through a cylindrical nanopore by Kesselheim et al. [Phys. Rev. Lett. 112, 018101 (2014)] have revealed that ions close to the surface of the DNA experience an additional friction contribution when compared to their bulk value. This friction is a key ingredient in reproducing the 2006 experimentally observed current modifications by Smeets and coworkers. While these findings were already incorporated into a coarse-grained model by Weik et al. [J. Chem. Phys. 145, 194106 (2016)], we now present an extended mean-field model for solving the electrokinetic equations of a dsDNA confined to a structureless cylindrical pore. This is done by incorporating a suitably constructed friction term into the Nernst-Planck equation. Solving the modified electrokinetic equations using a finite element method, we demonstrate that this model is able to reproduce experimental and atomistic MD results for dsDNA current modulations. The advantage of our model is that it allows a fast evaluation of new geometric arrangements of the DNA within the cylinder

Conformation and Dynamics of Long-Chain End-Tethered Polymers in Microchannels

Polyelectrolytes constitute an important group of materials, used for such different purposes as the stabilization of emulsions and suspensions or oil recovery. They are also studied and utilized in the field of microfluidics. With respect to the latter, a part of the interest in polyelectrolytes inside microchannels stems from genetic analysis, considering that deoxyribonucleic acid (DNA) molecules are polyelectrolytes. This review summarizes the single-molecule experimental and molecular dynamics simulation-based studies of end-tethered polyelectrolytes, especially addressing their relaxation dynamics and deformation characteristics under various external forces in micro-confined environments. In most of these studies, DNA is considered as a model polyelectrolyte. Apart from summarizing the results obtained in that area, the most important experimental and simulation techniques are explained

Conformation and Dynamics of Long-Chain End-Tethered Polymers in Microchannels

Polyelectrolytes constitute an important group of materials, used for such different purposes as the stabilization of emulsions and suspensions or oil recovery. They are also studied and utilized in the field of microfluidics. With respect to the latter, a part of the interest in polyelectrolytes inside microchannels stems from genetic analysis, considering that deoxyribonucleic acid (DNA) molecules are polyelectrolytes. This review summarizes the single-molecule experimental and molecular dynamics simulation-based studies of end-tethered polyelectrolytes, especially addressing their relaxation dynamics and deformation characteristics under various external forces in micro-confined environments. In most of these studies, DNA is considered as a model polyelectrolyte. Apart from summarizing the results obtained in that area, the most important experimental and simulation techniques are explained

ESPResSo 4.0 – an extensible software package for simulating soft matter systems

ESPResS