Asymmetric ion transport through "Janus" MoSSe sub-nanometer pores.

We conduct all-atom molecular dynamics simulations to systematically investigate the underlying mechanisms governing ion transport through a sub-nanometer pore decorated with negative charges in a "Janus" MoSSe membrane. The charge imbalance between S and Se atoms on each side of the membrane induces different types of ion adsorption processes depending on the pore inner charge configuration, and the polarity of external biases, which leads to asymmetry in ionic - characteristics. Statistical analysis of the total translocation times including adsorption-desorption processes, and ion dwell times indicates that potassium ions predominantly remain adsorbed during their interaction with the membrane before undertaking a quick translocation through the pore.

Ion Trapping and Thermionic Emission across Sub-nm Pores.

Ionic transport through a graphene biomimetic subnanometer (sub-nm) pore of arbitrary shape and realistically decorated by intrinsic negatively charged sites is investigated by all-atom molecular dynamics (MD) simulations. In the presence of external electric fields, cation trapping-assisted translocation occurs in the vicinity of the 2D subnanometer pore, while the anion current is blocked by the negative charges. The adsorbed cations in such asymmetrically charged nanopores are located on the top of the nanopore instead of blocking the pore, as suggested previously in highly symmetric pores such as crown ethers.

Ion Density-Dependent Dynamic Conductance Switching in Biomimetic Graphene Nanopores.

Gating in ion transport is at the center of many vital living-substance transmission processes, and understanding how gating works at an atomic level is essential but intricate. However, our understanding and finite experimental findings of subcontinuum ion transport in subnanometer nanopores are still limited, which is out of reach of the classical continuum nanofluidics. Moreover, the influence of ion density on subcontinuum ion transport is poorly understood.

Self-assembled microtubular electrodes for on-chip low-voltage electrophoretic manipulation of charged particles and macromolecules.

On-chip manipulation of charged particles using electrophoresis or electroosmosis is widely used for many applications, including optofluidic sensing, bioanalysis and macromolecular data storage. We hereby demonstrate a technique for the capture, localization, and release of charged particles and DNA molecules in an aqueous solution using tubular structures enabled by a strain-induced self-rolled-up nanomembrane (S-RuM) platform. Cuffed-in 3D electrodes that are embedded in cylindrical S-RuM structures and biased by a constant DC voltage are used to provide a uniform electrical field inside the microtubular devices.

Microscopic Detection Analysis of Single Molecules in MoS Membrane Nanopores.

A systematic microscopic analysis of the various resistive effects involved in the electronic detection of single biomolecules in a nanopore of a MoS nanoribbon is presented. The variations of the transverse electronic current along the two-dimensional (2D) membrane due to the translocation of DNA and protein molecules through the pore are obtained by model calculations based on molecular dynamics (MD) and Boltzmann transport formalism, which achieved good agreement with the experimental data. Our analysis points to a self-consistent interaction among ions, charge carriers around the pore rim, and biomolecules.

DNA punch cards for storing data on native DNA sequences via enzymatic nicking.

Synthetic DNA-based data storage systems have received significant attention due to the promise of ultrahigh storage density and long-term stability. However, all known platforms suffer from high cost, read-write latency and error-rates that render them noncompetitive with modern storage devices. One means to avoid the above problems is using readily available native DNA.

Classification of Epigenetic Biomarkers with Atomically Thin Nanopores.

We use the electronic properties of 2D solid-state nanopore materials to propose a versatile and generally applicable biosensor technology by using a combination of molecular dynamics, nanoscale device simulations, and statistical signal processing algorithms. As a case study, we explore the classification of three epigenetic biomarkers, the methyl-CpG binding domain 1 (MBD-1), MeCP2, and γ-cyclodextrin, attached to double-stranded DNA to identify regions of hyper- or hypomethylations by utilizing a matched filter. We assess the sensing ability of the nanopore device to identify the biomarkers based on their characteristic electronic current signatures.

Large Scale Parallel DNA Detection by Two-Dimensional Solid-State Multipore Systems.

We describe a scalable device design of a dense array of multiple nanopores made from nanoscale semiconductor materials to detect and identify translocations of many biomolecules in a massively parallel detection scheme. We use molecular dynamics coupled to nanoscale device simulations to illustrate the ability of this device setup to uniquely identify DNA parallel translocations. We show that the transverse sheet currents along membranes are immune to the crosstalk effects arising from simultaneous translocations of biomolecules through multiple pores, due to their ability to sense only the local potential changes.

Detection and Mapping of DNA Methylation with 2D Material Nanopores.

DNA methylation is an epigenetic modification involving the addition of a methyl group to DNA, which is heavily involved in gene expression and regulation, thereby critical to the progression of diseases such as cancer. In this work we show that detection and localization of DNA methylation can be achieved with nanopore sensors made of two-dimensional (2D) materials such as graphene and molybdenum di-sulphide (MoS). We label each DNA methylation site with a methyl-CpG binding domain protein (MBD1), and combine molecular dynamics simulations with electronic transport calculations to investigate the translocation of the methylated DNA-MBD1 complex through 2D material nanopores under external voltage biases.

Geometrical Effect in 2D Nanopores.

A long-standing problem in the application of solid-state nanopores is the lack of the precise control over the geometry of artificially formed pores compared to the well-defined geometry in their biological counterpart, that is, protein nanopores. To date, experimentally investigated solid-state nanopores have been shown to adopt an approximately circular shape. In this Letter, we investigate the geometrical effect of the nanopore shape on ionic blockage induced by DNA translocation using triangular h-BN nanopores and approximately circular molybdenum disulfide (MoS) nanopores.

Cascaded spintronic logic with low-dimensional carbon.

Remarkable breakthroughs have established the functionality of graphene and carbon nanotube transistors as replacements to silicon in conventional computing structures, and numerous spintronic logic gates have been presented. However, an efficient cascaded logic structure that exploits electron spin has not yet been demonstrated. In this work, we introduce and analyse a cascaded spintronic computing system composed solely of low-dimensional carbon materials.

Graphene Nanopores for Electronic Recognition of DNA Methylation.

We investigate theoretically the ability of graphene nanopore membranes to detect methylated sites along a DNA molecule by electronic sheet current along the two-dimensional (2D) materials. Special emphasis is placed on the detection sensitivity changes due to pore size, shape, position, and the presence of defects around the nanopore in a membrane with constricted geometry. Enhanced sensitivity for detecting methylated CpG sites, labeled by methyl-CpG binding domain (MBD) proteins along a DNA molecule, is obtained for electronic transport through graphene midgap states caused by the constriction.

Electrically Tunable Quenching of DNA Fluctuations in Biased Solid-State Nanopores.

Nanopores offer sensors for a broad range of nanoscale materials, in particular ones of biological origin such as single- and double-stranded DNA or DNA-protein complexes. In order to increase single-molecule sensitivity, it is desirable to control biomolecule motion inside nanopores. In the present study, we investigate how in the case of a double-stranded DNA the single-molecule sensitivity can be improved through bias voltages.

Intrinsic Stepwise Translocation of Stretched ssDNA in Graphene Nanopores.

We investigate by means of molecular dynamics simulations stretch-induced stepwise translocation of single-stranded DNA (ssDNA) through graphene nanopores. The intrinsic stepwise DNA motion, found to be largely independent of size and shape of the graphene nanopore, is brought about through alternating conformational changes between spontaneous adhesion of DNA bases to the rim of the graphene nanopore and unbinding due to mechanical force or electric field. The adhesion reduces the DNA bases' vertical conformational fluctuations, facilitating base detection and recognition.

Electronic structures of defects and magnetic impurities in MoS2 monolayers.

We provide a systematic and theoretical study of the electronic properties of a large number of impurities, vacancies, and adatoms in monolayer MoS2, including groups III and IV dopants, as well as magnetic transition metal atoms such as Mn, Fe, Co, V, Nb, and Ta. By using density functional theory over a 5 × 5 atomic cell, we identify the most promising element candidates for p-doping of MoS2. Specifically, we found VB group impurity elements, such as Ta, substituting Mo to achieve negative formation energy values with impurity states all sitting at less than 0.

Tunable graphene quantum point contact transistor for DNA detection and characterization.

A graphene membrane conductor containing a nanopore in a quantum point contact geometry is a promising candidate to sense, and potentially sequence, DNA molecules translocating through the nanopore. Within this geometry, the shape, size, and position of the nanopore as well as the edge configuration influences the membrane conductance caused by the electrostatic interaction between the DNA nucleotides and the nanopore edge. It is shown that the graphene conductance variations resulting from DNA translocation can be enhanced by choosing a particular geometry as well as by modulating the graphene Fermi energy, which demonstrates the ability to detect conformational transformations of a double-stranded DNA, as well as the passage of individual base pairs of a single-stranded DNA molecule through the nanopore.

Gate-Modulated Graphene Quantum Point Contact Device for DNA Sensing.

In this paper, we present a computational model to describe the electrical response of a constricted graphene nanoribbon (GNR) to biomolecules translocating through a nanopore. For this purpose, we use a self-consistent 3D Poisson equation solver coupled with an accurate three-orbital tight-binding model to assess the ability for a gate electrode to modulate both the carrier concentration as well as the conductance in the GNR. We also investigate the role of electrolytic screening on the sensitivity of the conductance to external charges and find that the gate electrode can either suppress or enhance the screening of biomolecular charges in the nanopore depending on the value of its potential.

Electronic detection of dsDNA transition from helical to zipper conformation using graphene nanopores.

Mechanical manipulation of DNA by forced extension can lead double-stranded DNA (dsDNA) to structurally transform from a helical form to a linear zipper-like form. By employing classical molecular dynamics and quantum mechanical nonequilibrium Green's function-based transport simulations, we show the ability of graphene nanopores to discern different dsDNA conformations, in a helical to zipper transition, using transverse electronic conductance. In particular, conductance oscillations due to helical dsDNA vanish as dsDNA extends from a helical form to a zipper form while it is transported through the nanopore.

Graphene quantum point contact transistor for DNA sensing.

By using the nonequilibrium Green's function technique, we show that the shape of the edge, the carrier concentration, and the position and size of a nanopore in graphene nanoribbons can strongly affect its electronic conductance as well as its sensitivity to external charges. This technique, combined with a self-consistent Poisson-Boltzmann formalism to account for ion charge screening in solution, is able to detect the rotational and positional conformation of a DNA strand inside the nanopore. In particular, we show that a graphene membrane with quantum point contact geometry exhibits greater electrical sensitivity than a uniform armchair geometry provided that the carrier concentration is tuned to enhance charge detection.

Slowing down and stretching DNA with an electrically tunable nanopore in a p-n semiconductor membrane.

We have studied single-stranded DNA translocation through a semiconductor membrane consisting of doped p and n layers of Si forming a p-n-junction. Using Brownian dynamics simulations of the biomolecule in the self-consistent membrane-electrolyte potential obtained from the Poisson-Nernst-Planck model, we show that while polymer length is extended more than when its motion is constricted only by the physical confinement of the nanopore. The biomolecule elongation is particularly dramatic on the n-side of the membrane where the lateral membrane electric field restricts (focuses) the biomolecule motion more than on the p-side.

Polymer translocation through an electrically tunable nanopore in a multilayered semiconductor membrane.

We have developed a two-level computational model that enables us to calculate electrostatic fields created by a semiconductor membrane submerged in electrolytic solution and investigate the effects of these fields on the dynamics of a polymer translocating through a nanopore in the membrane. In order to calculate the electrostatic potentials and the ionic concentrations in a solid-state nanopore, we have self-consistently solved Poisson equation within the semiclassical approximation for charge carrier statistics in the membrane and electrolyte. The electrostatic potentials obtained from these simulations are then used in conjunction with Langevin (Brownian) dynamics to model polymer translocation through the nanopore.

Computational investigation of DNA detection using graphene nanopores.

Nanopore-based single-molecule detection and analysis have been pursued intensively over the past decade. One of the most promising applications in this regard is DNA sequencing achieved through DNA translocation-induced blockades in ionic current. Recently, nanopores fabricated in graphene sheets were used to detect double-stranded DNA.

Defect symmetry influence on electronic transport of zigzag nanoribbons.

The electronic transport of zigzag-edged graphene nanoribbon (ZGNR) with local Stone-Wales (SW) defects is systematically investigated by first principles calculations. While both symmetric and asymmetric SW defects give rise to complete electron backscattering region, the well-defined parity of the wave functions in symmetric SW defects configuration is preserved. Its signs are changed for the highest-occupied electronic states, leading to the absence of the first conducting plateau.

On the sensing mechanism in carbon nanotube chemiresistors.

There has been recent controversy whether the response seen in carbon nanotube (CNT) chemiresistors is associated with a change in the resistance of the individual nanotubes or changes in the resistance of the junctions. In this study, we carry out a network analysis to understand the relative contributions of the nanotubes and the junctions to the change in resistance of the nanotube network. We find that the dominant mode of detection in nanotube networks changes according to the conductance level (defect level) in the nanotubes.

Chirality effects in atomic vacancy-limited transport in metallic carbon nanotubes.

We use first principles density functional theory combined with nonequilibrium Green's function technique to investigate the electronic and transport properties of metallic armchair and zigzag carbon nanotubes (CNTs) with different kinds of multivacancy defects. While the existence of a small band gap in pristine zigzag (12,0) CNTs lowers its conductance compared to pristine armchair (7,7) CNTs, transport properties in the presence of multi (hexa)-vacancy are superior in the former nanostructure, that is more sensitive to defect size and topology than the latter. In addition, in the zigzag structures hexavacancy nanotubes have higher conductance than divancancy nanotubes, which is due to the presence of midgap states that reduce the transmission gap and enhance the conductance.