Single Molecule Spectroscopy

With the advent of Next-Generation-Sequencing (NGS) technologies, an enormous volume of DNA sequencing data in excess of one billion short reads per instrument per day can be generated at low cost, placing genomic science within the grasp of everyday medicine. Mired in this voluminous data, a new problem has emerged: the assembly of the genome from the short reads. De novo assembly is an NP-hard problem and repetitive segments longer than the read length are the crux of the matter. It becomes exponentially harder to assemble a genome as the number of repeats grows. We propose to develop a nanopore device for de novo sequencing of a single DNA molecule with very long (>1 kbp) reads. Nanopore sequencing has the potential for very long reads, reducing the computational burden posed by alignment and genome assembly, while at the same time eliminating logistically challenging and error-prone amplification and library formation due to its exquisite single molecule sensitivity. Nanopore sequencing relies on the electrolytic current that develops when a DNA molecule, immersed in electrolyte, is forced by an electric field to translocate through a pore. Each nucleotide in the pore presents an energy barrier to the passage of ions, which blocks the current through the pore in a characteristic way. However, long, high fidelity reads demand stringent control over both the DNA configuration in the pore and the translocation kinetics. The configuration determines how the ions passing through the pore contact the nucleotides which affect the signal, while the kinetics affect the time allowed for data acquisition. Read Full Article >

Synthetic Biology

Quorum sensing (QS) is a prime example of paracrine signaling in which a cell affects gene expression in a neighboring cell. According to the classic QS hypothesis, bacteria communicate and count their numbers by producing, releasing, and detecting small, diffusible, signaling molecules called autoinducers (AI). Quorum-sensing has also been implicated in the regulation of processes such as bioluminescence, swarming, swimming, and virulence. But despite its appeal, the QS hypothesis may not be an accurate description of all these phenomenon. Read Full Article >



(a) A scanning electron micrograph of a MOSFET tester (metal contacts to the Source, Gate, and Drain shown here). The cross section of the MOSFET (blue dashed line) is shown in Fig. (b). (b) A transmission electron micrograph of one finger of a nominally 30nm gate length nMOSFET with a 1.3nm thick gate oxide. The gate is comprised of heavily doped polysilicon 95nm thick with a CoSi2 strap. The 40nm sidewalls consist of a 10nm thick oxide beneath 30nm of silicon nitride. A magnified view of the area outlined in red is shown in Fig. (c). The gate oxide in appears to be about 1.3nm thick.

Mobile/(broadband) wireless communications is changing everything. Portable communication devices like the cell phone, along with 3G, WLAN, Bluetooth¨ are spurring the demand for high frequency, mixed signal integrated circuits that are inexpensive, reliable and have a long battery life. CMOS technology can satisfy these demands. The relentless scaling of CMOS toward nanometer-scale gate lengths has produced MOSFETs with digital and RF performance that is suitable for mixed-signal applications. Read Full Article >

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