Publications

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We discuss chemical, structural, and ellipsometry characterization of low temperature epitaxial Si. While low temperature growth is not ideal, we are still able to prepare crystalline Si to cap functional atomic precision devices.

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We describe an all-optical lithography process that can make electrical contact to nanometer-precision donor devices fabricated in silicon using scanning tunneling microscopy (STM). This is accomplished by implementing a cleaning procedure in the STM that allows the integration of metal alignment marks and ion-implanted contacts at the wafer level. Low-temperature transport measurements of a patterned device establish the viability of the process.

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Optical fluorescence-based DNA assays are commonly used for pathogen detection and consist of an optical substrate containing DNA capture molecules, binding of target RNA or DNA sequences, followed by detection of the hybridization event with a fluorescent probe. Though fluorescence detection can offer exquisite signal-to-background ratios, with high specificity, vast opportunities exist to improve current optical-based genomic sensing approaches. For these reasons, there is a clear need to explore alternative optical sensing paradigms to alleviate these restrictions. Bio-templated nanomaterial synthesis has become a powerful concept for developing new platforms for bio-sensing, as the biomolecule of interest can act as part of the sensing transducer mechanism. We explored the use of DNA origami structures to immobilize gold nanoparticles in very precise localized arrangements producing unique optical absorption properties with implications in novel DNA sensing schemes. We also explored the use of in-situ TEM as a novel characterization method for DNA-nanoparticle assemblies.

Bioweapons and emerging infectious diseases pose growing threats to our national security. Both natural disease outbreak and outbreaks due to a bioterrorist attack are a challenge to detect, taking days after the outbreak to identify since most outbreaks are only recognized through reportable diseases by health departments and reports of unusual diseases by clinicians. In recent decades, arthropod-borne viruses (arboviruses) have emerged as some of the most significant threats to human health. They emerge, often unexpectedly, from cryptic transmission foci causing localized outbreaks that can rapidly spread to multiple continents due to increased human travel and trade. Currently, diagnosis of acute infections requires amplification of viral nucleic acids, which can be costly, highly specific, technically challenging and time consuming. No diagnostic devices suitable for use at the bedside or in an outbreak setting currently exist. The original goals of this project were to 1) develop two highly sensitive and specific diagnostic assays for detecting RNA from a wide range of arboviruses; one based on an electrochemical approach and the other a fluorescent based assay and 2) develop prototype microfluidic diagnostic platforms for preclinical and field testing that utilize the assays developed in goal 1. We generated and characterized suitable primers for West Nile Virus RNA detection. Both optical and electrochemical transduction technologies were developed for DNA-RNA hybridization detection and were implemented in microfluidic diagnostic sensing platforms that were developed in this project.