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Innovation Grants Program, 2008

Electrical Detection of Biomolecules Using Functionalized Semiconductor Nanowires

Cherie R. Kagan
Department of Electrical and Systems Engineering

(co-PI) Christopher B. Murray
Department of Chemistry



Semiconductor NWs will be functionalized with small molecule linkers and helical proteins that selectively recognize biomolecular analytes. NWs are electrostatically trapped in transistor structures and the electrical characteristics will be used to measure analyte capture.

This research program is focused on chemically synthesized semiconductor nanowires (NWs) functionalized with small molecule linkers or helical proteins to provide recognition sites for electrical detection of biomolecular analytes. The semiconductor NWs will be electrostatically trapped in three-terminal junctions to make transistors and the electrical characteristics will be used as an indicator of analyte capture and biomolecular affinity. In a liquid cell test structure, we will explore the dynamics and limits of sensitivity ultimately targeting single molecule electrical detection, to correlate electrical and optical detection methods, and to provide selectivity through molecular recognition of biomolecules using functionalized semiconductor NWs.


Synthesis and Assembly of DNA Block-copolymers


So-Jung Park
Department of Chemistry

The high-density conjugation of DNA on nanoparticle surfaces can bring about unusual biological properties (i.e., sharp melting transition and high thermal stability of DNA duplex), that are very useful in DNA detection applications. We propose to utilize DNA block-copolymers and their ability to self-assemble with nanoparticles to functionalize various types of nanoparticles with DNA. Importantly, the resulting co-assemblies should have an ultrahigh DNA density at the exterior of the assemblies, which should lead to the extraordinary DNA hybridization properties mentioned above.


Photoconductivity Studies in Nanoparticle Arrays and the Development of Linker Molecules for Efficient Inter-particle Coupling

Marija Drndic
Department of Physics and Astronomy


Nanocrystals (or quantum dots) are nanometer-size crystals and they are important systems for nanoscience in general. The objective of this study is to understand the phototransport in devices of nanoparticles and to develop their device applications. Appropriate surface functionalization is often the key factor for many nanoparticle applications as it governs the inter-particle coupling and therefore, the basic optical and electronic properties of nanoparticle-based devices. For example, ligands affect nanoparticle assembly and how closely nanoparticles can pack on surfaces. This project will investigate photoconductivity in nanocrystal arrays and design linker molecules for efficient inter-particle coupling.


Electro-active Polymers/CNT Composites as a New Active Media for Supercapacitors

Jorge J. Santiago-Avilés
Department of Electrical and Systems Engineering


Electropolymerization of ProDOT at Platinum (red) and PNES-SWNT-modified Platinum (black) electrodes. The electropolymerization at the PNES-SWNT film-modified surfaces demonstrated superior charge capacity properties compared to those observed at Pt electrodes.

The redox processes in electroactive polymers (EAPs) makes possible their use for the construction of charge storage devices like supercapacitors. Advantages such as reduced cost and environmental impact of EAPs relative to traditional metal oxide-based active materials underscore the attractiveness of organic supercapacitor composites. Furthermore, properties of EAPs, such as conductivity, voltage window, storage capacity, and chemical stability can be tailored via chemical modification. This project explores the performance of a new class of hybrid materials, polymer-wrapped single wall carbon nanotubes (SWNTs), to established EAP poly(3,4-propylenedioxythiophene) (PProDOT)-based anode and cathode material benchmarks. These polymer-wrapped SWNT composites exploit rigid, polyanionic-poly(arylenethynylene)s which provide unusual solubility and dispersion characteristics for carbon nanotubes. The fabrication of these composite materials, along with their potentiometric properties, impedance characteristics, thermo-mechanical features, redox kinetics, and charge transport properties will be studied.

Probing the Single Molecule Ligand-receptor Interaction by Synthetic Molecular Tip

Yoko Yamakoshi
Department of Radiology


Non-covalent interactions (molecular recognitions) play an important role in the expression of biological activity, and the small organic molecules that modulate these activities are critical for drug discovery.  Our aspect of our research is ligand-receptor interaction analysis by atomic force microscopy (AFM), which is modified with an organic molecular tip on its cantilever.  New types of molecular tips with a tripod structure are synthesized and AFM force measurements allow us to interrogate the interaction of small molecules with transmembrane receptors at the single molecule scale.


Dynamics of Unfolding Coiled-coil Proteins in Microfluidic Devices: Theory and Experiments

Prashant K. Purohit
Department of Mechanical Engineering and Applied Mechanics

(co PI) Paulo E. Arratia
Department of Mechanical Engineering and Applied Mechanics


Stretching DNA in a microfluidic device. (a)-(e) Time lapse images of fluorescently labeled DNA being stretched. (f) Normalized length of the molecule as a function of time. The black curve is obtained by integrating the conservation of momentum equation (see text) and the pink points are data from the experiment. (g) Coiled-coil proteins that we propose to stretch in a microfluidic device.

The main goal of this research is to characterize the sequential unfolding of coiled-coil proteins under applied external forces through experiments and theory. Fundamental research in coiled-coil proteins will be applied to intermediate filaments such as vimentin and desmin, whose mechanics is central to the pathogenesis of diseases such as muscular dystrophy and premature ageing. In this work, experiments will be performed using a two-phase flow and fluids of different viscosities in order to drive coiled-coil protein molecules away from their equilibrium folded state. Molecules will be visualized using single molecule fluorescent methods. Molecule extension will be measured as a function of strain rate and viscous drag (i.e. force). We will also develop a continuum model to understand the mechanical behavior of coiled-coil proteins both in traditional atomic force microscope (AFM) pulling experiments as well as in fluid flow. The continuum model will be based on a multi-well free energy density that allows multiple metastable configurations to exist under a given state of stress and temperature. Experimental data obtained from single molecule experiments in microfluidic devices will be compared to the continuum model.


Nano/Bio Interface Center @ The University of Pennsylvania
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