PPDiffuse: A Quantitative Prediction Tool for Diffusion of Charged Polymers in a Nanopore

Nanopore-based sensing of charged biopolymers is a powerful single-molecule method. In aconventional nanopore experiment, a single biological (proteinaceous) or solid-state nanopore perforates a thin membrane that is wetted by, and electrically isolates, two opposing reservoirs of electrolyte solution. A potential is applied across the membrane via external electronics coupled to the electrolyte reservoirs with electrochemical electrodes, actuating the system. The electric field set up by the applied potential in the nanopore and its immediate environment plays two roles: supporting an ionic current through the nanopore, which reports on the properties of the pore and its contents; and acting on analyte molecules to attract them to, and drive them into, the nanopore. The presence of a large biopolymer in the pore modulates the ionic current 𝐼(𝑡). The duration of the ionic current modulation corresponds to the length of time the polymer spends in the pore from capture to its ultimate escape, either by retraction to the reservoir from which it was captured, or by translocation to the opposite reservoir . The probabilities of retraction or translocation, or splitting probabilities, and the corresponding distributions of escape times (𝑡esc), are particularly sensitive to the size and charge of the analyte molecule and have been the focus of much theoretical, computational, and experimental effort. An underlying physical framework in which the distribution of escape times is modeled as a first-passage time from a one-dimensional potential is quantitatively predictive for a wide range of experiments. The complexity of this potential for the general case, however, requires calculations to guide experimental design that can be tedious to implement. PPDiffuse is intended to remove this burden from the nanopore research community and enable convenient, rational design of nanopore experiments with complex substrates such as polypeptides.

Structural, capacitive and energy characteristics of electrochemical electrodes based on polyaniline/multi-walled carbon nanotube nanocomposites

Polyaniline nanocomposites with nitrogen-doped multiwalled carbon nanotubes, initial and functionalized argon ions are prepared by the in-situ chemical oxidative polymerization of aniline. The morphology of obtained nanocomposites are studied by microscopic methods. The capacitive and energy characteristics of electrochemical electrodes formed by pressing nanocomposites have been studied by cyclic voltammetry. It is shown that an electrode based on a nanocomposite with functionalized nanotubes has the highest specific capacity and energy due to the high porosity of the surface. However, the low mechanical strength of this electrode leads to a decrease in its cyclic stability

Effect of An Image Resolution Change on the Effective Transport Coefficient of Heterogeneous Materials

Electrochemical electrodes comprise multiple phenomena at different scales. Several works have tried to model such phenomena using statistical techniques. This paper proposes a novel process to work with reduced size images to reconstruct microstructures with the Simulated Annealing method. Later, using the Finite Volume Method, it is verified the effect of the image resolution on the effective transport coefficient (ETC). The method can be applied to synthetic images or images from the Scanning Electron Microscope. The first stage consists of obtaining the image of minimum size, which contains at least 98% of the statistical information of the original image, allowing an equivalent statistical study. The image size reduction was made by applying an iterative decimation over the image using the normalized coarseness to compare the amount of information contained at each step. Representative improvements, especially in processing time, are achieved by reducing the size of the reconstructed microstructures without affecting their statistical behavior. The process ends computing the conduction efficiency from the microstructures. The simulation results, obtained from two kinds of images from different materials, demonstrate the effectivity of the proposed approach. It is important to remark that the controlled decimation allows a reduction of the processor and memory use during the reconstruction and ETC computation of electrodes.

Parallel 1024-ch Cyclic Voltammetry on Monolithic CMOS Electrochemical Detector Array

Large-scale microelectrode arrays offers enhanced spatiotemporal resolution in electrophysiology studies.. In this paper, we discuss the design and performance of an electrochemical detector array which is capable of 1024-ch parallel cyclic voltammetry (CV) as well as other electrochemical measurements. The electrochemical detector is fabricated using a custom-designed CMOS chip which integrates both the circuity and on-chip microelectrode array, to operate and record from electrochemical measurements. For parallel 1024-ch recordings, 1024 capacitor-based integrating transimpedance amplifiers (TIA) are designed and integrated. The TIA design features the bipolar capabilities for measuring both negative and positive electrochemical currents due to reduction and oxidation of molecules. The resulted dynamic range of this TIA is −700 pA – 1968 pA. CV can be used to examine the quality of electrochemical electrodes by measuring the double-layer capacitance. Double-layer capacitance forms at the electrode-electrolyte interface and is a function of the effective area of the electrode. Thus, a contaminated electrode can have smaller effective area resulting in smaller double-layer capacitance. Using the parallel CV capability of the monolithic CMOS device, the double layer capacitance of all 1024 electrodes are simultaneously measured to examine the status of the electrodes’ surface in real time. The initial measurement of the electrode array showed a mean capacitance of 466 pF. After plasma treatment to remove contamination on the electrode’s surface, the increased capacitance was 1.36nF nearly tripling the effective surface area. We have successfully developed of 1024-ch electrochemical detector array using the monolithic CMOS sensor. The CV functionality was validated by measuring the double-layer capacitance of the on-chip electrode array. This method can accelerate the characterization of a massive electrode array before analytical experiments to provide well-controlled electrochemical electrodes, which is crucial in conducting reliable electrochemical measurements.

Designing ionic channels in novel carbons for electrochemical energy storage

Tremendous efforts have been dedicated to developing high-performance energy storage devices based on the micro- or nano-manipulation of novel carbon electrodes, as certain nanocarbons are perceived to have advantages such as high specific surface areas, superior electric conductivities, excellent mechanical properties and so on. In typical electrochemical electrodes, ions are intercalated/deintercalated into/from the bulk (for batteries) or adsorbed/desorbed on/from the surface (for electrochemical capacitors). Fast ionic transport, significantly determined by ionic channels in active electrodes or supporting materials, is a prerequisite for the efficient energy storage with carbons. In this report, we summarize recent design strategies for ionic channels in novel carbons and give comments on the promising features based on those carbons towards tailorable ionic channels.