Ratcheting Charged Polymers through Symmetric Nanopores Using Pulsed Fields: Designing a Low Pass Filter for Concentrating Polyelectrolytes.

We present a new concept for the separation of DNA molecules by contour length that combines a nanofluidic ratchet, nanopore translocation, and pulsed fields. Using Langevin dynamics simulations, we show that it is possible to design pulsed field sequences to ratchet captured semiflexible molecules in such a way that only short chains successfully translocate, effectively transforming the nanopore process into a low pass molecular filter. We also show that asymmetric pulses can significantly enhance the device efficiency.

A numerical investigation of analyte size effects in nanopore sensing systems.

We investigate the ionic current modulation in DNA nanopore translocation setups by numerically solving the electrokinetic mean-field equations for an idealized model. Specifically, we study the dependence of the ionic current on the relative length of the translocating molecule. Our simulations show a significantly smaller ionic current for DNA molecules that are shorter than the pore at low salt concentrations.

Modeling the current modulation of bundled DNA structures in nanopores.

We investigate the salt-dependent current modulation of bundled DNA nanostructures in a nanopore. To this end, we developed four simulation models for a 2 × 2 origami structure with increasing level of detail ranging from the mean-field level to an all-atom representation of the DNA structure. We observe a consistent pore conductivity as a function of salt concentration for all four models.

The influence of motility on bacterial accumulation in a microporous channel.

We study the transport of bacteria in a porous media modeled by a square channel containing one cylindrical obstacle via molecular dynamics simulations coupled to a lattice Boltzmann fluid. Our bacteria model is a rod-shaped rigid body which is propelled by a force-free mechanism. To account for the behavior of living bacteria, the model also incorporates a run-and-tumble process.

Erratum: Modeling Gel Swelling Equilibrium in the Mean Field: From Explicit to Poisson-Boltzmann Models [Phys. Rev. Lett. 122, 208002 (2019)].

This corrects the article DOI: 10.1103/PhysRevLett.122.

Modeling Gel Swelling Equilibrium in the Mean Field: From Explicit to Poisson-Boltzmann Models.

We develop a double mean-field theory for charged macrogels immersed in electrolyte solutions in the spirit of the cell model approach. We first demonstrate that the equilibrium sampling of a single explicit coarse-grained charged polymer in a cell yields accurate predictions of the swelling equilibrium if the geometry is suitably chosen and all pressure contributions have been incorporated accurately. We then replace the explicit flexible chain by a suitably modeled penetrable charged rod that allows us to compute all pressure terms within the Poisson-Boltzmann approximation.

A computational model for bacterial run-and-tumble motion.

In this article we present a computational model for the simulation of self-propelled anisotropic bacteria. To this end we use a self-propelled particle model and augment it with a statistical algorithm for the run-and-tumble motion. We derive an equation for the distribution of reorientations of the bacteria that we use to analyze the statistics of the random walk and that allows us to tune the behavior of our model to the characteristics of an E.

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.

Relaxation of surface-tethered polymers under moderate confinement.

We study the relaxation of surface-tethered polymers in microchannels under moderate confinement (i.e. h ∼ Rg, where h is the channel height and Rg is the radius of gyration of the polymer) by experiments with fluorescence-marked DNA molecules and coupled lattice-Boltzmann/molecular dynamics simulations.

Electric-field-induced stretching of surface-tethered polyelectrolytes in a microchannel.

We study the stretching of a surface-tethered polyelectrolyte confined between parallel surfaces under the application of a dc electric field. We explore the influence of the electric-field strength, the length of the polyelectrolyte, and the degree of confinement on the conformation of the polyelectrolyte by single-molecule experiments and coarse-grained coupled lattice-Boltzmann molecular-dynamics simulations. The fractional extension of the polyelectrolyte is found to be a universal function of the product of the applied electric field and the molecular contour length, which is explained by simple scaling arguments.

Stretching of surface-tethered polymers in pressure-driven flow under confinement.

We study the effect of pressure-driven flow on a single surface-tethered DNA molecule confined between parallel surfaces. The influence of flow and channel parameters as well as the length of the molecules on their extension and orientation is explored. In the experiments the chain conformations are imaged by laser scanning confocal microscopy.

The stretching force on a tethered polymer in pressure-driven flow.

We use mesoscopic lattice-Boltzmann/molecular dynamics simulations to study the stretching behavior of a single tethered polymer in micro- and nanochannels. In particular, we are interested in the connection between fluid flow properties and the force on the polymer chain. An analytical expression for the stretching force is proposed, which linearly depends on the number of monomers and the boundary shear rate.