Coarse-grained simulation of polymer translocation through an artificial nanopore

The translocation of a macromolecule through a nanometer-sized pore is an interesting process with important applications in the development of biosensors for single--molecule analysis and in drug delivery and gene therapy. We have carried out a molecular dynamics simulation study of electrophoretic translocation of a charged polymer through an artificial nanopore to explore the feasibility of semiconductor--based nanopore devices for ultra--fast DNA sequencing. The polymer is represented by a simple bead--spring model designed to yield an appropriate coarse-grained description of the phosphate backbone of DNA in salt--free aqueous solution. A detailed analysis of single translocation event is presented to assess whether the passage of individual ions through the pore can be detected by a nanoscale field--effect transistor by measuring variations in electrostatic potential during polymer translocation. We find that it is possible to identify single events corresponding to the passage of counterions through the pore, but that discrimination of individual ions on the polymer chain based on variations in electrostatic potential is problematic. Several distinct stages in the translocation process are identified, characterized by changes in polymer conformation and by variations in the magnitude and direction of the internal electric field induced by the fluctuating charge distribution. The dependence of the condensed fraction of counterions on Bjerrum length leads to significant changes in polymer conformation, which profoundly affect the dynamics of electrophoresis and translocation.Comment: 37 pages Revtex, 11 postscript figure

Dielectric spectroscopy of ferroelectric nematic liquid crystals: Measuring the capacitance of insulating interfacial layers

Numerous measurements of the dielectric constant $\epsilon$ of the recently discovered ferroelectric nematic ($N_F$) liquid crystal (LC) phase report extraordinarily large values of $\epsilon^\prime$ (up to ~30,000). We show that what is in fact being measured in such experiments is the high capacitance of the non-ferroelectric, interfacial, insulating layers of nanoscale thickness that bound the $N_F$ material in typical cells. We analyze a parallel-plate cell filled with $N_F$ material of high-polarization $\mathbf{P}$, oriented parallel to the plates at zero applied voltage. Minimization of the dominant electrostatic energy renders $\mathbf{P}$ spatially uniform and orients it to make the electric field in the $N_F$ as small as possible, a condition under which the voltage applied to the cell appears almost entirely across the high-capacity interfacial layers. This coupling of orientation and charge creates a combined polarization-external capacitance (PCG) Goldstone reorientation mode requiring applied voltages orders of magnitude smaller than that of the $N_F$ layer alone to effectively transport charge across the $N_F$ layer. The $N_F$ layer acts as a low-value resistor and the interfacial capacitors as reversible energy storage reservoirs, lowering the restoring force (mass) of the PCG mode and producing strong reactive dielectric behavior. Analysis of data from several experiments on ferroelectric liquid crystals (chiral smectics C, bent-core smectics, and the $N_F$ phase supports the PCG model, showing deriving that deriving dielectric constants from electrical impedance measurements of high-polarization ferroelectric LCs, without properly accounting for the self-screening effects of polarization charge and the capacitive contributions of interfacial layers, can result in overestimation of the $\epsilon^\prime$ values of the LC by many orders of magnitude.Comment: 26 pages of text, 10 figures, 49 references (40 pages total