Identifying SARS-CoV-2 Variants Using Single-Molecule Conductance Measurements.

The global COVID-19 pandemic has highlighted the need for rapid, reliable, and efficient detection of biological agents and the necessity of tracking changes in genetic material as new SARS-CoV-2 variants emerge. Here, we demonstrate that RNA-based, single-molecule conductance experiments can be used to identify specific variants of SARS-CoV-2. To this end, we (i) select target sequences of interest for specific variants, (ii) utilize single-molecule break junction measurements to obtain conductance histograms for each sequence and its potential mutations, and (iii) employ the XGBoost machine learning classifier to rapidly identify the presence of target molecules in solution with a limited number of conductance traces.

Electronic Properties of DNA Origami Nanostructures Revealed by Calculations.

DNA origami is a pioneering approach for producing complex 2- or 3-D shapes for use in molecular electronics due to its inherent self-assembly and programmability properties. The electronic properties of DNA origami structures are not yet fully understood, limiting the potential applications. Here, we conduct a theoretical study with a combination of molecular dynamics, first-principles, and charge transmission calculations.

Ion detection in a DNA nanopore FET device.

An ion detection device that combines a DNA-origami nanopore and a field-effect transistor (FET) was designed and modeled to determine sensitivity of the nanodevice to the local cellular environment. Such devices could be integrated into a live cell, creating an abiotic-biotic interface integrated with semiconductor electronics. A continuum model is used to describe the behavior of ions in an electrolyte solution.

Charge transport through DNA with energy-dependent decoherence.

Modeling charge transport in DNA is essential to understand and control the electrical properties and develop DNA-based nanoelectronics. DNA is a fluctuating molecule that exists in a solvent environment, which makes the electron susceptible to decoherence. While knowledge of the Hamiltonian responsible for decoherence will provide a microscopic description, the interactions are complex and methods to calculate decoherence are unclear.

DNA nanopores as artificial membrane channels for bioprotonics.

Biological membrane channels mediate information exchange between cells and facilitate molecular recognition. While tuning the shape and function of membrane channels for precision molecular sensing via de-novo routes is complex, an even more significant challenge is interfacing membrane channels with electronic devices for signal readout, which results in low efficiency of information transfer - one of the major barriers to the continued development of high-performance bioelectronic devices. To this end, we integrate membrane spanning DNA nanopores with bioprotonic contacts to create programmable, modular, and efficient artificial ion-channel interfaces.

DNA-Au (111) interactions and transverse charge transport properties for DNA-based electronic devices.

DNA's charge transfer and self-assembly characteristics have made it a hallmark of molecular electronics for the past two decades. A fast and efficient charge transfer mechanism with programmable properties using DNA nanostructures is required for DNA-based nanoelectronic applications and devices. The ability to integrate DNA with inorganic substrates becomes critical in this process.

Metal-Mediated DNA Nanotechnology in 3D: Structural Library by Templated Diffraction.

DNA double helices containing metal-mediated DNA (mmDNA) base pairs are constructed from Ag and Hg ions between pyrimidine:pyrimidine pairs with the promise of nanoelectronics. Rational design of mmDNA nanomaterials is impractical without a complete lexical and structural description. Here, the programmability of structural DNA nanotechnology toward its founding mission of self-assembling a diffraction platform for biomolecular structure determination is explored.

Computational study of the role of counterions and solvent dielectric in determining the conductance of B-DNA.

DNA naturally exists in a solvent environment, comprising water and salt molecules such as sodium, potassium, magnesium, etc. Along with the sequence, the solvent conditions become a vital factor determining DNA structure and thus its conductance. Over the last two decades, researchers have measured DNA conductivity both in hydrated and almost dry (dehydrated) conditions.

A Spin-Dependent Model for Multi-Heme Bacterial Nanowires.

The electrical properties of conductive heme-based nanowires found in bacteria were investigated using spin-dependent density functional theory (DFT). Molecular orbitals were generated using a restricted open-shell model which was solved by applying constraints to the spin-separated unrestricted open-shell model. Charge transport was simulated at different length scales ranging from individual heme sites up to the monomer unit of the nanowire, looking at hopping and tunneling between neighboring heme porphyrins with different Fe oxidation states.

Performance analysis of DNA crossbar arrays for high-density memory storage applications.

Deoxyribonucleic acid (DNA) has emerged as a promising building block for next-generation ultra-high density storage devices. Although DNA has high durability and extremely high density in nature, its potential as the basis of storage devices is currently hindered by limitations such as expensive and complex fabrication processes and time-consuming read-write operations. In this article, we propose the use of a DNA crossbar array architecture for an electrically readable read-only memory (DNA-ROM).

Metal-Mediated DNA Nanotechnology in 3D: Structural Library by Templated Diffraction.

DNA double helices containing metal-mediated DNA (mmDNA) base pairs have been constructed from Ag and Hg ions between pyrimidine:pyrimidine pairs with the promise of nanoelectronics. Rational design of mmDNA nanomaterials has been impractical without a complete lexical and structural description. Here, we explore the programmability of structural DNA nanotechnology toward its founding mission of self-assembling a diffraction platform for biomolecular structure determination.

A machine learning approach for accurate and real-time DNA sequence identification.

Background: The all-electronic Single Molecule Break Junction (SMBJ) method is an emerging alternative to traditional polymerase chain reaction (PCR) techniques for genetic sequencing and identification. Existing work indicates that the current spectra recorded from SMBJ experimentations contain unique signatures to identify known sequences from a dataset. However, the spectra are typically extremely noisy due to the stochastic and complex interactions between the substrate, sample, environment, and the measuring system, necessitating hundreds or thousands of experimentations to obtain reliable and accurate results.

Role of intercalation in the electrical properties of nucleic acids for use in molecular electronics.

Intercalating ds-DNA/RNA with small molecules can play an essential role in controlling the electron transmission probability for molecular electronics applications such as biosensors, single-molecule transistors, and data storage. However, its applications are limited due to a lack of understanding of the nature of intercalation and electron transport mechanisms. We addressed this long-standing problem by studying the effect of intercalation on both the molecular structure and charge transport along the nucleic acids using molecular dynamics simulations and first-principles calculations coupled with the Green's function method, respectively.

Detection and identification of genetic material via single-molecule conductance.

The ongoing discoveries of RNA modalities (for example, non-coding, micro and enhancer) have resulted in an increased desire for detecting, sequencing and identifying RNA segments for applications in food safety, water and environmental protection, plant and animal pathology, clinical diagnosis and research, and bio-security. Here, we demonstrate that single-molecule conductance techniques can be used to extract biologically relevant information from short RNA oligonucleotides, that these measurements are sensitive to attomolar target concentrations, that they are capable of being multiplexed, and that they can detect targets of interest in the presence of other, possibly interfering, RNA sequences. We also demonstrate that the charge transport properties of RNA:DNA hybrids are sensitive to single-nucleotide polymorphisms, thus enabling differentiation between specific serotypes of Escherichia coli.

Nanoink bridge-induced capillary pen printing for chemical sensors.

Single-walled carbon nanotubes (SWCNTs) are used as a key component for chemical sensors. For miniature scale design, a continuous printing method is preferred for electrical conductance without damaging the substrate. In this paper, a non-contact capillary pen printing method is presented by the formation of a nanoink bridge between the nib of a capillary pen and a polyethylene terephthalate film.

Gunn-Hilsum Effect in Mechanically Strained Silicon Nanowires: Tunable Negative Differential Resistance.

Gunn (or Gunn-Hilsum) Effect and its associated negative differential resistivity (NDR) emanates from transfer of electrons between two different energy subbands. This effect was observed in semiconductors like GaAs which has a direct bandgap of very low effective mass and an indirect subband of high effective mass which lies ~300 meV above the former. In contrast to GaAs, bulk silicon has a very high energy spacing (~1 eV) which renders the initiation of transfer-induced NDR unobservable.

Comparing Charge Transport in Oligonucleotides: RNA:DNA Hybrids and DNA Duplexes.

Understanding the electronic properties of oligonucleotide systems is important for applications in nanotechnology, biology, and sensing systems. Here the charge-transport properties of guanine-rich RNA:DNA hybrids are compared to double-stranded DNA (dsDNA) duplexes with identical sequences. The conductance of the RNA:DNA hybrids is ∼10 times higher than the equivalent dsDNA, and conformational differences are determined to be the primary reason for this difference.

Zero-bias photocurrents in highly-disordered networks of Ge and Si nanowires.

Semiconducting nanowire (NW) devices have garnered attention in self-powered electronic and optoelectronic applications. This work explores and exhibits, for the first time for visible light, clear evidence of the zero-biased optoelectronic switching in randomly dispersed Ge and Si NW networks. The test bench, on which the NWs were dispersed for optoelectronic characterization, was fabricated using a standard CMOS fabrication process, and utilized metal contacts with dissimilar work functions-Al and Ni.

Conformational gating of DNA conductance.

DNA is a promising molecule for applications in molecular electronics because of its unique electronic and self-assembly properties. Here we report that the conductance of DNA duplexes increases by approximately one order of magnitude when its conformation is changed from the B-form to the A-form. This large conductance increase is fully reversible, and by controlling the chemical environment, the conductance can be repeatedly switched between the two values.

Programmable diode/resistor-like behavior of nanostructured vanadium pentoxide xerogel thin film.

Electrical properties of a Cr/V2O5/Cr structure are investigated and switching of the device due to electrochemical reactions is observed at low bias (<1 V). Depending on the polarity of the first applied bias, the switched device can behave like a diode (forward sweep first) or a resistor (reverse sweep first). The switching is irreversible and persistent, lasting for more than one month.

The role of cytosine methylation on charge transport through a DNA strand.

Cytosine methylation has been found to play a crucial role in various biological processes, including a number of human diseases. The detection of this small modification remains challenging. In this work, we computationally explore the possibility of detecting methylated DNA strands through direct electrical conductance measurements.

Negative differential resistance in boron nitride graphene heterostructures: physical mechanisms and size scaling analysis.

Hexagonal boron nitride (hBN) is drawing increasing attention as an insulator and substrate material to develop next generation graphene-based electronic devices. In this paper, we investigate the quantum transport in heterostructures consisting of a few atomic layers thick hBN film sandwiched between graphene nanoribbon electrodes. We show a gate-controllable vertical transistor exhibiting strong negative differential resistance (NDR) effect with multiple resonant peaks, which stay pronounced for various device dimensions.

Junction-less phototransistor with nanowire channels, a modeling study.

We propose a new nanowire based, junction-less phototransistor, that consists of a channel with both wide and narrow regions to ensure efficient light absorption and low dark current, respectively. While the light is absorbed in the wide region, the narrow region allows for ease of band engineering. We also find that a nanowire in the source can further boost the optical gain.

H+-type and OH- -type biological protonic semiconductors and complementary devices.

Proton conduction is essential in biological systems. Oxidative phosphorylation in mitochondria, proton pumping in bacteriorhodopsin, and uncoupling membrane potentials by the antibiotic Gramicidin are examples. In these systems, H(+) hop along chains of hydrogen bonds between water molecules and hydrophilic residues - proton wires.