Search results for "nanopore"
showing 10 items of 99 documents
Improving the Design of Ion Track-Based Biosensors
2018
In the last decade we had developed new types of biosensors, by cladding the inner walls of transparent etched swift heavy ion tracks in thin polymer foils with enzymes. The enzymatic reaction products of appropriate analytes penetrating into narrow tracks are enriched in the track’s confinement, and they change the electrical track properties if their charge states differ from those of the analytes. It was yet unknown how to design these sensors so that their best efficiency and highest possible sensitivity is achieved. This requires the accurate knowledge of the optimum track radius and the degree of product enrichment within the tracks. These questions were answered by appropriate experi…
Current rectification by nanoparticle blocking in single cylindrical nanopores.
2014
Blocking of a charged pore by an oppositely charged nanoparticle can support rectifying properties in a cylindrical nanopore, as opposed to the usual case of a fixed asymmetry in the pore geometry and charge distribution. We present here experimental data and model calculations to confirm this fundamental effect. The nanostructure imaging and the effects of nanoparticle concentration, pore radius, and salt concentration on the electrical conductance–voltage (G–V) curves are discussed. Logic responses based on chemical and electrical inputs/outputs could also be implemented with a single pore acting as an effective nanofluidic diode. To better show the generality of the results, different ch…
Capillary Rise in Nanopores: Molecular Dynamics Evidence for the Lucas-Washburn Equation
2007
When a capillary is inserted into a liquid, the liquid will rapidly flow into it. This phenomenon, well studied and understood on the macroscale, is investigated by Molecular Dynamics simulations for coarse-grained models of nanotubes. Both a simple Lennard-Jones fluid and a model for a polymer melt are considered. In both cases after a transient period (of a few nanoseconds) the meniscus rises according to a $\sqrt{\textrm{time}}$-law. For the polymer melt, however, we find that the capillary flow exhibits a slip length $\delta$, comparable in size with the nanotube radius $R$. We show that a consistent description of the imbibition process in nanotubes is only possible upon modification o…
Silicatein conjugation inside nanoconfined geometries through immobilized NTA–Ni(ii) chelates
2013
The chemical modification and bioconjugation processes inside confined geometries by His-tagged silicatein promote sensitive changes in the polarity and surface charge density that mainly contribute to the ionic current rectification properties of the single conical nanopores.
Label-free histamine detection with nanofluidic diodes through metal ion displacement mechanism
2017
[EN] We design and characterize a nanofluidic device for the label-free specific detection of histamine neurotransmitter based on a metal ion displacement mechanism. The sensor consists of an asymmetric polymer nanopore fabricated via ion track-etching technique. The nanopore sensor surface having metal-nitrilotriacetic (NTA-Ni2+) chelates is obtained by covalent coupling of native carboxylic acid groups with N-alpha,N-alpha-bis(carboxymethyl)-L-lysine (BCML), followed by exposure to Ni2+ ion solution. The BCML immobilization and subsequent Ni2+ ion complexation with NTA moieties change the surface charge concentration, which has a significant impact on the current-voltage (I-V) curve after…
Ejection of a Polymer Chain from a Nanopore: Theory and Computer Experiment
2010
We consider the ejection dynamics of a flexible polymer chain out of confined environment. This situation arises in different physical contexts, including a flexible synthetic polymer partially confined in a nanopore and a viral genome partially ejected from its capsid. We describe the chain release from confinement both analytically and by means of dynamic Monte Carlo simulation. We find two distinct regimes of ejection dynamics depending on whether the chain is fully or partially confined. Partially confined chains are ejected from a pore of length L and diameter D after a typical time τ ∝ L2D5/3, regardless of their contour length N. The process is driven by a constant force f ≈ 5kBT/D a…
Out of Equilibrium Characteristics of a Forced Translocating Chain through a Nanopore
2009
Polymer translocation through a nano-pore in a thin membrane is studied using a coarse-grained bead-spring model and Langevin dynamics simulation with a particular emphasis to explore out of equilibrium characteristics of the translocating chain. We analyze the out of equilibrium chain conformations both at the $cis$ and the $trans$ side separately either as a function of the time during the translocation process or as as function of the monomer index $m$ inside the pore. A detailed picture of translocation emerges by monitoring the center of mass of the translocating chain, longitudinal and transverse components of the gyration radii and the end to end vector. We observe that polymer confi…
Monte Carlo simulations of the 2d-Ising model in the geometry of a long stripe
2011
Abstract The two-dimensional Ising model in the geometry of a long stripe can be regarded as a model system for the study of nanopores. As a quasi-one-dimensional system, it also exhibits a rather interesting “phase behavior”: At low temperatures the stripe is either filled with “liquid” or “gas” and “densities” are similar to those in the bulk. When we approach a “pseudo-critical point” (below the critical point of the bulk) at which the correlation length becomes comparable to the length of the stripe, several interfaces emerge and the systems contains multiple “liquid” and “gas” domains. The transition depends on the size of the stripe and occurs at lower temperatures for larger stripes.…
Converting external potential fluctuations into nonzero time-average electric currents using a single nanopore
2015
The possibility of taking advantage of a fluctuating environment for energy and information transduction is a significant challenge in biological and artificial nanostructures. We demonstrate here directional electrical transduction from fluctuating external signals using a single nanopore of conical shape immersed in an ionic aqueous solution. To this end, we characterize experimentally the average output currents obtained by the electrical rectification of zero time-average input potentials. The transformation of external potential fluctuations into nonzero time-average responses using a single nanopore in liquid state is of fundamental significance for biology and nanophysics. This energ…
A Monte Carlo Study of Knots in Long Double-Stranded DNA Chains.
2016
We determine knotting probabilities and typical sizes of knots in double-stranded DNA for chains of up to half a million base pairs with computer simulations of a coarse-grained bead-stick model: Single trefoil knots and composite knots which include at least one trefoil as a prime factor are shown to be common in DNA chains exceeding 250,000 base pairs, assuming physiologically relevant salt conditions. The analysis is motivated by the emergence of DNA nanopore sequencing technology, as knots are a potential cause of erroneous nucleotide reads in nanopore sequencing devices and may severely limit read lengths in the foreseeable future. Even though our coarse-grained model is only based on …