Session N44: Focus Session: Translocation through Nanopores II

How tension propagates for a driven semi-flexible chain while translocating through a nano-pore

Driven translocation of a stiff chain through a nano-pore is studied using Langevin dynamics in two dimension (2D). We observe that for a given chain length $N$ the mean first passage time (MFPT) $\langle \tau \rangle$ increases for a stiffer chain and the translocation exponent $\alpha$ ($\langle \tau \rangle \sim N^\alpha$) satisfies the inequality $2\nu < \alpha < 1+\nu$, where $\nu$ is the equilibrium Flory exponent for a given chain stiffness. We calculate the residence time of the individual monomers and observe that the peak position of the residence time $W(m)$ as a function of the monomer index $m$ shifts at a \textit{lower} $m$-value with \textit{increasing chain stiffness $\kappa_b$}. Finally, we provide qualitative physical explanation for dependence of various quantities on chain stiffness $\kappa_b$ by using ideas from Sakaue's tension propagation(TP) theory [Phys. Rev. E {\bf 76}, 021803 (2007)] and its recent implementation into a Brownian dynamics tension propagation (BDTP) scheme for a finite chain by Ikonen et al. [J. Chem. Phys. {\bf 137}, 085101 (2012); Phys. Rev. E {\bf 85}, 051803 (2012)]for a semi-flexible chain.   

Experimental measurements of the rate of capture of synthetic and natural polyelectrolytes by alpha-hemolysin under salt concentration gradients

We report experimental data on the effect of gradients in salt concentration on the capture rate of synthetic and natural polyelectrolytes by the alpha-hemolysin pore under an electric field. We find that the capture rate is nonmonotonic with the ratio of salt concentration in the trans to that in the cis. We have also determined the extent of the nonmonotonicity at different pH conditions. Our results present challenges for an understanding of the phenomenon.   

Linear and ring DNA macromolecules moderately and strongly confined in nanochannels

Understanding the mechanism of DNA extension in nanochannels is necessary for interpretation of experiments in nanofluidic channel devices that are conducted recently not only with linear but also with ring chains. Except reviewing the situation with linear chains we analyze here the experimental results and simulations for the channel-induced extension (linearization) of ring chains. Results of simulations for confined rings indicate that similar transition between moderate and strong confinement as in the case of linear chains exists also for rings. Due to stronger self-avoidance in confined rings the transition and relative chain extension is shifted in comparison to linear DNA. We suggest that similar relation as used in experiments for the extension of linear chains may be used also for circular DNA. For linear DNA in channel relatively stable distinctive events due to chain backfolding, which complicate chain linearization experiments, are analyzed. The abundance of DNA chains folded at the chain ends and in the chain interior was analyzed as a function of the channel width. Z. Benkova, P.Cifra, Macromolecules 45, 2597-2608 (2012) P. Cifra, T.Bleha, Soft Matter 8, 9022-9028 (2012)   

Polymer Translocation in a Crowded Environment: Effects due to Obstacle Density and Arrangement

The translocation of a polymer across a membrane through a nanopore has received much attention, primarily due to emerging nanotechnology applications such as DNA sequencing. However, translocation is also a process that is ubiquitous in the natural world with examples including the transport of DNA and proteins across cell walls. Considering this latter motivation, the environment in which translocation occurs is relatively complicated with many intracellular and extracellular inclusions such as the cell organelles, soluble proteins, and components of the cytoskeleton and extracellular matrix. In this talk, we examine translocation in such a crowded environment via computer simulations in which we place immobile, spherical ``obstacles'' on both sides of the membrane. We show that an effective driving force arises i) when the concentration of obstacles across the pore differs and ii) when the arrangement of obstacles across the pore differs. A simple force model is used to estimate the magnitude of these entropic driving forces. Good agreement is found between the results and the simple models. Simulations are also performed with both effects present such that a bias resulting from a lower concentration of obstacles on the $cis$ side of the membrane is opposed by a bias arising from an increased amount of disorder on $trans$. Results from this setup indicate that in a real system where both effects are likely to play a role, it could be difficult to guess even the direction of the intrinsic resulting driving force, let alone the magnitude. We also present results from simulations in which the obstacles are mobile but restricted to different degrees.   

Electric field controlled small molecule transport through vertically aligned large diameter multiwalled carbon nanotube forest membrane

Vertically aligned multi-walled carbon nanotube (MWCNT) forest based porous membranes have been fabricated. The average inner diameter of the CNT is about 7 nm and the length is about 45 $\mu $m. The translocation behaviors of small charged molecules and gold nanoparticles through the CNT membrane under electric field have been investigated. Electrophoresis is found to be the main mechanism for the translocation of small molecules under the applied electric field in the range of 10000 Vm$^{-1}$. The interactions between the molecule and the hydrophobic CNT inner surface play an important role for the transport of small molecules. The chemical modifications at CNT ends can also effectively regulate the transport of molecules.   

Electric-field driven translocation of colloidal wild-type and mutant fd viruses through a solid-state nanopore

Colloidal suspensions of fd viruses are useful model systems for condensed matter physics. Here we explore the transport processes of fd particles in solid-state nanopores. Recently we have observed a nonlinear behavior in the electrophoretic mobility of wild-type fd particles. Here we carried out a comparative study of wild-type and mutant Y21M in their translocation dynamics through a nanopore. This work was supported by NSF-DMR and NSF-MRSEC.   

Polymer Translocation Dynamics in the Quasi-Static Limit

Monte Carlo and Langevin dynamics simulations are used to study the dynamics of polymer translocation through a nanopore using a coarse-grained model. We examine the relationship between the translocation free energy barrier and the translocation times through a comparison of the simulation results to predictions using the Fokker-Planck formalism. We illustrate the importance of using free energy profiles obtained from precise numerical calculations rather than those obtained from simple theoretical models. In addition, we determine the parameter regime within which the Focker-Planck approach is valid and beyond which non-equilibrium effects become appreciable. The relevance of these results to recent theoretical and simulation studies of polymer translocation dynamics is discussed.   

Nonequilibrium Dynamics of Polymer Translocation

When a flexible chain is pulled or sucked, it can initially respond only locally, and sequential nonequilibrium processes with large conformational distortion follow in line with the propagation of tensile force along the chain backbone. This is a generic dynamical response property of polymers, the understanding of which provides us with a viewpoint to capture an essential aspect of the driven translocation process. In the meeting, I will summarize a basic framework to analyze the nonequilibrium dynamics of driven translocation process alongside of recent progresses. \\[4pt] References:\\[0pt] T. Sakaue, Phys. Rev. E, 76, 021803 (2007) ``Nonequilibrium dynamics of polymer translocation and straightening''\\[0pt] T. Sakaue, Phys. Rev. E, 81, 041808 (2010) ``Sucking genes into pores: Insight into driven translocation''\\[0pt] T. Saito and T. Sakaue, Eur. Phys. J. E, 34, 145 (2011) ``Dynamical diagram and scaling in polymer driven translocation''\\[0pt] T. Saito and T. Sakaue, Phys. Rev. E, 85, 061803 (2012) ``Process time distribution of driven polymer transport''   

Active Control of Protein and Ionic Transport through Semiconducting Conical Nanopores

Nanopores with conical geometries have been found to rectify ionic current in electrolytes. While nanopores in semiconducting membranes offer the ability to modulate ionic transport, the fabrication of conical nanopores in silicon has proven challenging. Here, we report the discovery that Au nanoparticle-assisted plasma etching results in the formation of conical etch profiles in Si [1]. We show that this process provides a versatile means to fabricate nanopores on Si substrates with variable pore-diameters and cone-angles. When in contact with aqueous electrolyte solution (pH\textgreater 3), the nanopore was found to exhibit negative surface charge due to de-protonation of the Si-OH surface groups. The rectification ratio of ionic current through the pore was thus found to be variable by altering the pH, owing to the amphoteric nature of Si-OH surface groups (pKa 6.9) and was also dependent on the ionic strengths, agreeing with the theoretical predictions based on Poisson$-$Nernst$-$Planck equation. We demonstrate that these semiconducting conical nanopores can function as ionic switches with high on-off ratios, by varying Si surface charge through voltage gating. Further, we demonstrate voltage gated control over protein translocation through these pores. [1]. Voltage-gated ion transport through semiconducting conical nanopores formed by metal nanoparticle assisted plasma etching, T. James, \textit{et al.} Nano Letters 12, 7, 3437--3442 (2012).   

Rapid fabrication of sub-5nm solid-state nanopore for low cost biosensing

Nanopores-based technologies are emerging as a powerful tool for single molecule analysis. They are also the leading candidates for future generation DNA sequencing platforms. Despite all of these potentials, current solid-state nanopore fabrication techniques, based on focused beams of energetic particles, remains low throughput, complex and expensive. Such drawbacks greatly limit the breadth of applications, and are major barriers to commercialization of any nanopore-based technologies. We have demonstrated a simple, highly scalable and low cost method to fabricate solid-state nanopores. It relies on stressing a thin dielectric membrane with high-electric field while submerged in aqueous salt solution. The technique allows a single sub-5nm nanopore be fabricated within a minute directly in liquids. In addition, a pore can be precisely enlarged by the similar used of high-electric field stressing. We will describe the fabrication method, present our current understanding of the physical mechanism leading to pore formation, and demonstrate its usefulness for single-molecule detection by studying DNA translocation kinetics. The discovery of this new method opens a wide range of possibilities for single-molecule biophysics and commercial sensing applications.   

Probing the Influence of Coil Configuration on DNA Translocation Dynamics in Solid-State Nanopores

We studied electrophoretic DNA translocations of asymmetric nanopore-cavity structures designed to control the initial configurations of molecules. The structures comprise a thin SiN membrane with a nanopore that leads into a 400 nm-high cavity, which is in turn covered by a 400-nm thick SiN membrane with a circular opening whose diameter ranged from 150\,nm to 1.5\,$\mu$m. These structures maintain a gap between the nanopore and a DNA coil translocating from above, but not one translocating from below. The viscous drag on the DNA segment extending from the coil to the nanopore significantly slowed translocations from above. The mean translocation times for those events were 2.5 times longer than for tranlocations from below when the upper opening of the cavity was only 200\,nm wide. The translocation times converged as the opening was increased to micrometer diameters. This last result can be explained by the DNA coil, whose radius of gyration is $\sim$600\,nm, squeezing into the upper opening by increasing amounts. Our experimental results compare favourably with a quantitative model of DNA translocation speeds, similar to models by Lu \emph{et al.} and by Grosberg, which accounts for the initial configuration of the DNA coil.