Time-domain event detection using single-instruction, multiple-thread gpGPU architectures in single-molecule biophysical data.

Discrete amplitude levels in ordered, time-domain data often represent different underlying latent states of the system that is being interrogated. Analysis and feature extraction from these data sets generally require considering the order of each individual point; this approach cannot take advantage of contemporary general-purpose graphics processing units (gpGPU) and single-instruction multiple-data (SIMD) instruction set architectures. Two sources of such data from single-molecule biological measurements are nanopores and single-molecule field effect transistor (smFET) nanotube devices; both generate streams of time-ordered current or voltage data, typically sampled near 1 MS/s, with run times of minutes, yielding terabyte-scale datasets. Here, we present three gpGPU-based algorithms to overcome limitations associated with serial event detection in time series data, resulting in a 250× improvement in the rate with which we can detect salient features in nanopore and smFET datasets. The code is freely available.

Carbon-nanotube field-effect transistors for resolving single-molecule aptamer-ligand binding kinetics.

Small molecules such as neurotransmitters are critical for biochemical functions in living systems. While conventional ultraviolet-visible spectroscopy and mass spectrometry lack portability and are unsuitable for time-resolved measurements in situ, techniques such as amperometry and traditional field-effect detection require a large ensemble of molecules to reach detectable signal levels. Here we demonstrate the potential of carbon-nanotube-based single-molecule field-effect transistors (smFETs), which can detect the charge on a single molecule, as a new platform for recognizing and assaying small molecules. smFETs are formed by the covalent attachment of a probe molecule, in our case a DNA aptamer, to a carbon nanotube. Conformation changes on binding are manifest as discrete changes in the nanotube electrical conductance. By monitoring the kinetics of conformational changes in a binding aptamer, we show that smFETs can detect and quantify serotonin at the single-molecule level, providing unique insights into the dynamics of the aptamer-ligand system. In particular, we show the involvement of G-quadruplex formation and the disruption of the native hairpin structure in the conformational changes of the serotonin-aptamer complex. The smFET is a label-free approach to analysing molecular interactions at the single-molecule level with high temporal resolution, providing additional insights into complex biological processes.

Mixed-Dimensional 1D/2D van der Waals Heterojunction Diodes and Transistors in the Atomic Limit.

Inverting a semiconducting channel is the basis of all field-effect transistors. In silicon-based metal-oxide-semiconductor field-effect transistors (MOSFETs), a gate dielectric mediates this inversion. Access to inversion layers may be granted by interfacing ultrathin low-dimensional semiconductors in heterojunctions to advance device downscaling. Here we demonstrate that monolayer molybdenum disulfide (MoS2) can directly invert a single-walled semiconducting carbon nanotube (SWCNT) transistor channel without the need for a gate dielectric. We fabricate and study this atomically thin one-dimensional/two-dimensional (1D/2D) van der Waals heterojunction and employ it as the gate of a 1D heterojunction field-effect transistor (1D-HFET) channel. Gate control is based on modulating the conductance through the channel by forming a lateral p-n junction within the CNT itself. In addition, we observe a region of operation exhibiting a negative static resistance after significant gate tunneling current passes through the junction. Technology computer-aided design (TCAD) simulations confirm the role of minority carrier drift-diffusion in enabling this behavior. The resulting van der Waals transistor architecture thus has the dual characteristics of both field-effect and tunneling transistors, and it advances the downscaling of heterostructures beyond the limits of dangling bonds and epitaxial constraints faced by III-V semiconductors.

Unsupported planar lipid membranes formed from mycolic acids of Mycobacterium tuberculosis.

The cell wall of mycobacteria includes a thick, robust, and highly impermeable outer membrane made from long-chain mycolic acids. These outer membranes form a primary layer of protection for mycobacteria and directly contribute to the virulence of diseases such as tuberculosis and leprosy. We have formed in vitro planar membranes using pure mycolic acids on circular apertures 20 to 90 µm in diameter. We find these membranes to be long lived and highly resistant to irreversible electroporation, demonstrating their general strength. Insertion of the outer membrane channel MspA into the membranes was observed indicating that the artificial mycolic acid membranes are suitable for controlled studies of the mycobacterial outer membrane and can be used in nanopore DNA translocation experiments.

Silicon-on-sapphire integrated waveguides for the mid-infrared.

Silicon waveguides are now widely used to guide radiation in the near-infrared, mainly in the wavelength range of 1.1 - 2.2 microm. While low-loss waveguides at longer wavelengths in silicon have been proposed, experimental realization has been elusive. Here we show that single-mode integrated silicon-on-sapphire waveguides can be used at mid-infrared wavelengths. We demonstrate waveguiding at 4.5 microm, or 2222.2 cm(-1), with losses of 4.3 +/- 0.6 dB/cm. This result represents the first practical integrated waveguide system for the mid-infrared in silicon, and enables a range of new applications.