Dynamics of polymer translocation through nanopores: theory meets experiment

The dynamics of translocation of polymer molecules through nanopores is investigated via molecular dynamics. We find that an off-lattice minimalist model of the system is sufficient to reproduce quantitatively all the experimentally observed trends and scaling behavior. Specifically, simulations show (i) two translocation regimes depending on the ratio of pore and polymer length, (ii) two different regimes for the probability of translocation depending on applied voltage, (iii) an exponential dependence of translocation velocity upon applied voltage, and (iv) an exponential decrease of the translocation time with temperature. We also propose a simple theoretical explanation of each of the observed trends within a free energy landscape framework.     

Polymer translocation through nanopores: Parking lot problems,scaling laws and their breakdown

The passage of a polymer through a narrow pore is associated with the crossing of a significant free energy barrier. Both in nature and in single molecule experiments the polymer is typically driven through the pore. We here address two such driving modes: (i) the driving by binding proteins that prevent (partial) back-sliding through the pore; and (ii) the driving by a trans-membrane force. In case (i) we derive the effective force and show finite size effects due to the size of the binding proteins. In case (ii) we demonstrate the crossover from a slow, equilibrium driving to a non-equilibrium behaviour at fast driving.     

Theoretical studies and molecular dynamics simulations on ion transport properties in nanochannels and nanopores

Control of ion transport and fluid flow through nanofluidic devices is of primary importance for energy storage and conversion, drug delivery and a wide range of biological processes. Recent development of nanotechnology, synthesis techniques, purification technologies, and experiment have led to rapid advances in simulation and modeling studies on ion transport properties. In this review, the applications of Poisson–Nernst–Plank(PNP) equations in analyzing transport properties are presented. The molecular dynamics(MD) studies of transport properties of ion and fluidic flow through nanofluidic devices are reported as well.     

Cooperative translocation dynamics of biopolymer chains through nanopores in a membrane: Slow dynamics limit

The cooperative translocation dynamics of two complementary single-stranded DNA chains through two nanopores located in a membrane is investigated theoretically. The translocation process is considered to be quasi-equilibrium, and then under the limit of slow dynamics the average translocation times are numerically presented under different conditions. It is shown that the effects of the chemical potential gradient, the recombination energy and the distance between the two nanopores on the cooperative translocation are significant. The present model predicts that the cooperative translocation of such two chains can shorten the translocation time, reduce the backward motion and thus improve the translocation efficiency.     

Sequence dependence of DNA translocation through a nanopore

We investigate the dynamics of DNA translocation through a nanopore using 2D Langevin dynamics simulations, focusing on the dependence of the translocation dynamics on the details of DNA sequences. The DNA molecules studied in this work are built from two types of bases A and C, which have been shown previously to have different interactions with the pore. We study DNA with repeating blocks A(n)C(n) for various values of n and find that the translocation time depends strongly on the block length 2n as well as on the orientation of which base enters the pore first. Thus, we demonstrate that the measurement of translocation dynamics of DNA through a nanopore can yield detailed information about its structure. We have also found that the periodicity of the block sequences is contained in the periodicity of the residence time of the individual nucleotides inside the pore.     

Compression and free expansion of single DNA molecules in nanochannels

We investigated compression and ensuing expansion of long DNA molecules confined in nanochannels. Transverse confinement of DNA molecules in the nanofluidic channels leads to elongation of their unconstrained equilibrium configuration. The extended molecules were compressed by electrophoretically driving them into porelike constrictions inside the nanochannels. When the electric field was turned off, the DNA strands expanded. This expansion, the dynamics of which has not previously been observable in artificial systems, is explained by a model that is a variation of de Gennes's polymer model.     

Statics and dynamics of single DNA molecules confined in nanochannels

The successful design of nanofluidic devices for the manipulation of biopolymers requires an understanding of how the predictions of soft condensed matter physics scale with device dimensions. Here we present measurements of DNA extended in nanochannels and show that below a critical width roughly twice the persistence length there is a crossover in the polymer physics.     

Translocation of DNA molecules through nanopores with salt gradients: the role of osmotic flow

Recent experiments of translocation of double-stranded DNA through nanopores [M. Wanunu et al., Nature Nanotech. 5, 160 (2009)] reveal that the DNA capture rate can be significantly influenced by a salt gradient across the pore. We show that osmotic flow combined with electrophoretic effects can quantitatively explain the experimental data on the salt-gradient dependence of the capture rate.     

DNA in nanopores: counterion condensation and coion depletion

Molecular dynamics simulations are used to study the equilibrium distribution of monovalent ions in a nanopore connecting two water reservoirs separated by a membrane, both for the empty pore and that with a single stranded DNA molecule inside. In the presence of DNA, the counterions condense on the stretched macromolecule effectively neutralizing it, and nearly complete depletion of coions from the pore is observed. The implications of our results for experiments on DNA translocation through alpha-hemolysin nanopores are discussed.     

Optical detection of DNA translocation through silicon nanopore by ultraviolet light

In this paper, we propose a new optical detection scheme for nanopore-based DNA sequencing with high resolution towards eventual base identification. We use ultraviolet light for excitation of a fluorescent probe attached to DNA and a nanopore in the silicon membrane that has a significantly large refractive index and an extinction coefficient at ultraviolet wavelengths. In this study, numerical electromagnetic simulation revealed that the z-polarization component (perpendicular to the membrane plane) of the electric field was dominant near the nanopore and generated a large electric field gradient at the nanopore exit, typically with a decay length of 2 nm for a nanopore with diameter of 7 nm. The large extinction coefficient contributed to reduction in background noise coming from fluorophore-labeled DNA strands that remain behind the membrane (the cis side of the membrane). We observed a high signal-to-noise ratio of single DNA translocation events under the application of an electric field.     

Pink noise of ionic conductance through single artificial nanopores revisited

We report voltage-clamp measurements through single conical nanopore obtained by chemical etching of a single ion track in polyimide film. Special attention is paid to the pink noise of the ionic current (i.e., 1/f noise) measured with different filling liquids. The relative pink-noise amplitude is almost independent of concentration and pH for KCl solutions, but varies strongly using ionic liquids. In particular, we show that depending on the ionic liquid, the transport of charge carriers is strongly facilitated (low noise and higher conductivity than in the bulk) or jammed. These results show that the origin of the pink noise can be ascribed neither to fluctuations of the pore geometry nor to the pore wall charges, but rather to a cooperative effect on ions motion in confined geometry.     

Concentration polarization and nonlinear electrokinetic flow near a nanofluidic channel

A perm-selective nanochannel could initiate concentration polarization near the nanochannel, significantly decreasing (increasing) the ion concentration in the anodic (cathodic) end of the nanochannel. Such strong concentration polarization can be induced even at moderate buffer concentrations because of local ion depletion (therefore thicker local Debye layer) near the nanochannel. In addition, fast fluid vortices were generated at the anodic side of the nanochannel due to the nonequilibrium electro-osmotic flow (EOF), which was at least approximately 10x faster than predicted from any equilibrium EOF. This result corroborates the relation among induced EOF, concentration polarization, and limiting-current behavior.     

Changes in polarization of Gaussian Schell-model beams and partially polarized Gaussian Schell-model beams through a polarization grating

The polarization properties of Gaussian Schell-model (GSM) beams and partially polarized Gaussian Schell-model (PGSM) beams passing through a polarization grating (PG) are studied based on the beam coherence-polarization (BCP) matrix formulism, where the finite size of the PG is considered. Detailed numerical calculation results are given and compared with the previous work.     

Reduced Coulomb repulsion in NMP-TCNQ through intra- and interchain polarization

The “bare” Coulomb repulsion between two delocalized electrons in a one-dimensional poly (TCNQ^?) chain of the organic charge transfer crystal NMP-TCNQ is shown to be substantially reduced by attractive terms arising (1) from the polarization of the localized electronic system of the TCNQ chain itself and (2) from the polarization of the delocalized electrons in neighbouring NMP chains. The resulting effective repulsion is 0.33 eV at the Fermi level.     

Electrical spin polarization through spin-momentum locking in topological-insulator nanostructures

Recently, spin-momentum-locked topological surface states(SSs) have attracted significant attention in spintronics.Owing to spin-momentum locking, the direction of the spin is locked at right angles with respect to the carrier momentum.In this paper, we briefly review the exotic transport properties induced by topological SSs in topological-insulator(TI)nanostructures, which have larger surface-to-volume ratios than those of bulk TI materials. We discuss the electrical spin generation in TIs and its effect on the transport properties. A current flow can generate a pure in-plane spin polarization on the surface, leading to a current-direction-dependent magnetoresistance in spin valve devices based on TI nanostructures.A relative momentum shift of two coupled topological SSs also generates net spin polarization and induces an in-plane anisotropic negative magnetoresistance. Therefore, the spin-momentum locking can enable the broad tuning of the spin transport properties of topological devices for spintronic applications.     

Size-dependent freezing of n-alcohols in silicon nanochannels

We present a study on the phase behavior of several linear n-alcohols (heptanol, nonanol and undecanol) in their bulk state as well as confined in mesoporous silicon. We were able to vary the mean pore radii of the nanochannels from r = 3.5  nm to 7 nm and to determine the respective temperatures of the freezing and melting transitions using infrared and dielectric spectroscopy. The smaller the chain length the lower the freezing point, both in the bulk and in the confined state. Under confinement the freezing temperature decreases by up to 28 K compared to the bulk value. In accordance with the Gibbs-Thompson model the lowering is proportional to the inverse pore radius, ΔT _fr ∝ 1/r. Moreover, the ratio of freezing temperature depression to melting temperature depression is close to the theoretical value of ΔT _fr /ΔT _melt = 3/2. The spectra also indicate a structural change: while the solid bulk alcohols are a polycrystalline mixture of the orthorhombic β- and monoclinic γ-form, geometrical confinement forces the alcohol-chains into the more simple orthorhombic structure. In addition, a part of the material does not crystallize. Such an additional amorphous phase seems to be a logical consequence of the size mismatch between molecular crystals and irregular shaped pores.     

Quenching spin decoherence in diamond through spin bath polarization

We experimentally demonstrate that the decoherence of a spin by a spin bath can be completely eliminated by fully polarizing the spin bath. We use electron paramagnetic resonance at 240 GHz and 8 T to study the electron-spin coherence time T2 of nitrogen-vacancy centers and nitrogen impurities in diamond from room temperature down to 1.3 K. A sharp increase of T2 is observed below the Zeeman energy (11.5 K). The data are well described by a suppression of the flip-flop induced spin bath fluctuations due to thermal electron-spin polarization. T2 saturates at approximately 250 micros below 2 K, where the polarization of the electron-spin bath exceeds 99%.