Molecular electrostatic potentials (MEPs) and vibrational electronics (“vibronics”) have developed into novel scenarios proposed by our group to process information at the molecular level. They along with the traditional current-voltage scenario can be used to design and develop molecular devices for the next generation electronics. Control and communication features of these scenarios strongly help in the production of “smart” devices able to take decisions and act autonomously in aggressive environments. In sensor science, the ultimate detector of an agent molecule is another molecule that can respond quickly and selectively among several agents. The purpose of this project is the design and development of molecular sensors based on the MEPs and vibronics scenarios to feature two different and distinguishable states of conductance, including a nano-micro interface to address and interconnect the output from the molecular world to standard micro-technologies. In this dissertation, theoretical calculations of the electrical properties such as the electron transport on molecular junctions are performed for the components of the sensor system. Proofs of concept experiments complement our analysis, which includes an electrical characterization of the devices and measurement of conductance states that may be useful for the sensing mechanism. In order to focus this work within the very broad array between nanoelectronic and molecular electronics, we define the new field of Molecular Engineering, which will have the mission to design molecular and atomistic devices and set them into useful systems. Our molecular engineering approach begins with a search for an optimum fit material to achieve the proposed goals; our published results suggest graphene as the best material to read signals from molecules, amplify the communication between molecular scenarios, and develop sensors of molecular agents with high sensitivity and selectivity. Specifically, this is possible in the case of sensors, thanks to the graphene atomic cross section (morphology), plasmonic surface (delocalized charge) and exceptional mechanical and electrical properties. Deliverables from this work are molecular devices and amplifiers able to read information encoded and processed at the molecular level and to amplify those signals to levels compatible with standard microelectronics. This design of molecular devices is a primordial step in the development of devices at the nanometer scale, which promises the next generation of sensors of chemical and biological agents molecularly sensitive, selective and intelligent.

This work details the attachment of dendrimers to proteins, peptides and single stranded DNA (ssDNA). Dendrimers based on melamine satisfy many of the synthetic demands in the field of bioconjugate chemistry including: monodispersity, synthetic flexibility and scalability. The solution-phase syntheses of both ssDNA-dendrimer and peptide-dendrimer bioconjugates is described, and thorough characterization by matrix-assisted laser desorption ionization/ time-of-flight (MALDI-TOF) mass spectrometry, UV-vis spectroscopy, fluorescence spectroscopy, and polyacrylamide gel electrophoresis is discussed. Non-covalent DNA-dendrimer complexes have been shown to facilitate antisense gene delivery, but are vulnerable to dissociation and subsequent enzymatic degradation within the cell. In an effort to prepare biocompatible antisense agents capable of effectively shielding ssDNA from intracellular nuclease digestion, disulfide-linked ssDNA-dendrimers were prepared and rigorously characterized to rule out the possibility of an electrostatic-based interaction. Hybridization assays were performed to determine if the covalently-attached dendrimer affected the ability of the attached ssDNA strand to anneal with a complementary sequence to form double-stranded DNA (dsDNA)-dendrimers. Results indicate that ssDNA-dendrimer conjugates readily anneal to complementary ssDNA strands either in solution or attached to gold surfaces. Nuclease digestions of conjugates in solution suggested that enzymatic manipulation of dsDNA-dendrimers is possible, offering promise for DNA-based computation and other fields of DNA-nanotechnology. Much larger bioconjugates consisting of dendrimers, proteins and peptides were prepared with the goal of obtaining molecular weights sufficient for enhanced permeability and retention (EPR) in tumors. While the dendrimer provides the advantages of a purely synthetic route for drug delivery, the protein portion of the bioconjugate provides a monodisperse, macromolecular scaffold for the non-covalent self-assembly of the dendrimers. The strategy presented herein is based on the strong interaction between biotin and the 60 kD tetrameric protein streptavidin. Each monomer of streptavidin is capable of binding 1 biotin molecule, thus when biotin functionalized peptide-dendrimers are added to streptavidin they bind to form a cluster of dendrimers, or a megamer. The biotinylated peptides that link the dendrimers to the streptavidin core provide a way to actively target specific cell types for drug delivery. Megamer formation through the addition of tetrameric streptavidin was successful as indicated by MALDI-TOF, UV-vis titration and gel electrophoresis assays.

Fluorescence resonance energy transfer (FRET)-based biosensors have been designed to fluorometrically detect everything from proteolytic activity to receptor-ligand interactions and structural changes in proteins. While a wide variety of fluorophores have demonstrated effectiveness in FRET probes, several potential sensor components are particularly notable. Semiconductor quantum dots (QDs) are attractive FRET donors because they are rather bright, exhibit high quantum yields, and their nanoparticulate structure enables the attachment of multiple acceptor molecules. Fluorescent proteins (FPs) are also of particular interest for fluorescent biosensors because design elements necessary for signal transduction, probe assembly, and device delivery and localization for intracellular applications can all be genetically incorporated into the FP polypeptide. The studies described in this thesis elucidate the important parameters for concerted QD-FP FRET probe design. Experimental results clarify issues of FRET pair selection, probe assembly, and donor-acceptor distance for the multivalent systems. Various analysis approaches are compared and guidelines asserted based on the results. To demonstrate the effectiveness of the QD-FP FRET probe platform, a ratiometric pH sensor is presented. The sensor, which uses the intrinsic pH-sensitivity of the FP mOrange to modulate the FP/QD emission ratio, exhibits a 20-fold change in its ratiometric measurement over a physiologically interesting pH range, making it a prime candidate for intracellular imaging applications.

Thesis (Ph. D.)--University of Missouri-Columbia, 2000. / Typescript. Vita. Includes bibliographical references. Also available on the Internet.

Thesis (Ph. D.)--UCLA, 2009. / Vita. Description based on print version record. Includes bibliographical references (leaves 347-368).

Thesis (Ph. D.)--University of Missouri-Columbia, 2000. / Typescript. Vita. Includes bibliographical references. Also available on the Internet.

Thesis (Ph. D.)--University of Chicago, Dept of Physics, August 2003. / Includes bibliographical references. Also available on the Internet.

Thesis (Ph. D.)--University of Oregon, 2003. / Typescript. Includes vita and abstract. Includes bibliographical references (leaves 146-153). Also available for download via the World Wide Web; free to University of Oregon users.

The rational and directed delivery of genetic material to the cell is a formidable tool to investigate the phenotypic effects of gene expression regulation and a promising therapeutic strategy for genetic defects. RNA interference constitutes a versatile approach to gene silencing. Despite the development of numerous strategies the transfection of small interfering RNA (siRNA) is highly dependent on cell type and conditions. Direct physical access to the intracellular compartment is a promising path for high efficiency delivery independently of cell type and conditions. Silicon nanowires grant such access with minimal toxic effects, and allow intracellular delivery of DNA when actuated by atomic force microscope. These findings reveal the potential for porous silicon nanostructures to serve as delivery vectors for nucleic acids due to their porous nature, elevated biocompatibility, and biodegradability. This dissertation illustrates the development a novel platform for efficient siRNA transfection based on an array of porous silicon nanoneedles. The synthesis of biodegradable and biocompatible porous nanowires was accomplished by a novel strategy for electroless etch of silicon that allows anisotropic etch simultaneously with porosification. An ordered array of cone shaped porous silicon nanoneedles with tunable tip size, array density and aspect ratio was obtained coupling this strategy with patterned metal deposition and selective reactive ion etch. This process also granted control over porosity, nanopore size and flexural modulus. The combination of these parameters was appropriately optimized to ensure cell penetration, maximize siRNA loading and minimize cytotoxic effects. Loading of the negatively charged siRNA molecules was optimized by applying an external electric field to the nanoneedles under appropriate voltage conditions to obtain a tenfold increase over open circuit loading, and efficient penetration of the siRNA within the porous volume of the needles. Alternative surface chemistry modification provided a means for effective siRNA loading and sustained release. siRNA transfection was achieved by either imprinting the nanoneedles array chip over a culture of MDA-MB-231 cells or allowing the cells to self-impale over the needles. The procedures allowed the needles to penetrate across the cell membrane without influencing cell proliferation. siRNA was successfully transfected and was effective at suppressing gene expression. / text

Over the last two decades, advanced fabrication techniques have enabled the fabrication of materials and devices at sub-micron length scales. For heat conduction, the conventional Fourier model for predicting energy transport has been shown to yield erroneous results on such length scales. In semiconductors and dielectrics, energy transport occurs through phonons, which are quanta of lattice vibrations. When phase coherence effects can be ignored, phonon transport may be modeled using the semi-classical phonon Boltzmann transport equation (BTE). The objective of this thesis is to develop an efficient computational method to solve the BTE, both for single-material and multi-material systems, where transport across heterogeneous interfaces is expected to play a critical role. The resulting solver will find application in the design of microelectronic circuits and thermoelectric devices. The primary source of computational difficulties in solving the phonon BTE lies in the scattering term, which redistributes phonon energies in wave-vector space. In its complete form, the scattering term is non-linear, and is non-zero only when energy and momentum conservation rules are satisfied. To reduce complexity, scattering interactions are often approximated by the single mode relaxation time (SMRT) approximation, which couples different phonon groups to each other through a thermal bath at the equilibrium temperature. The most common methods for solving the BTE in the SMRT approximation employ sequential solution techniques which solve for the spatial distribution of the phonon energy of each phonon group one after another. Coupling between phonons is treated explicitly and updated after all phonon groups have been solved individually. When the domain length is small compared to the phonon mean free path, corresponding to a high Knudsen number ([mathematical equation]), this sequential procedure works well. At low Knudsen number, however, this procedure suffers long convergence times because the coupling between phonon groups is very strong for an explicit treatment of coupling to suffice. In problems of practical interest, such as silicon-based microelectronics, for example, phonon groups have a very large spread in mean free paths, resulting in a combination of high and low Knudsen number; in these problems, it is virtually impossible to obtain solutions using sequential solution techniques. In this thesis, a new computational procedure for solving the non-gray phonon BTE under the SMRT approximation is developed. This procedure, called the coupled ordinates method (COMET), is shown to achieve significant solution acceleration over the sequential solution technique for a wide range of Knudsen numbers. Its success lies in treating phonon-phonon coupling implicitly through a direct solution of all equations in wave vector space at a particular spatial location. To increase coupling in the spatial domain, this procedure is embedded as a relaxation sweep in a geometric multigrid. Due to the heavy computational load at each spatial location, COMET exhibits excellent scaling on parallel platforms using domain decomposition. On serial platforms, COMET is shown to achieve accelerations of 60 times over the sequential procedure for Kn<1.0 for gray phonon transport problems, and accelerations of 233 times for non-gray problems. COMET is then extended to include phonon transport across heterogeneous material interfaces using the diffuse mismatch model (DMM). Here, coupling between phonon groups occurs because of reflection and transmission. Efficient algorithms, based on heuristics, are developed for interface agglomeration in creating coarse multigrid levels. COMET is tested for phonon transport problems with multiple interfaces and shown to outperform the sequential technique. Finally, the utility of COMET is demonstrated by simulating phonon transport in a nanoparticle composite of silicon and germanium. A realistic geometry constructed from x-ray CT scans is employed. This composite is typical of those which are used to reduce lattice thermal conductivity in thermoelectric materials. The effective thermal conductivity of the composite is computed for two different domain sizes over a range of temperatures. It is found that for low temperatures, the thermal conductivity increases with temperature because interface scattering dominates, and is insensitive to temperature; the increase of thermal conductivity is primarily a result of the increase in phonon population with temperature consistent with Bose-Einstein statistics. At higher temperatures, Umklapp scattering begins to take over, causing a peak in thermal conductivity and a subsequent decrease with temperature. However, unlike bulk materials, the peak is shallow, consistent with the strong role of interface scattering. The interaction of phonon mean free path with the particulate length scale is examined. The results also suggest that materials with very dissimilar cutoff frequencies would yield a thermal conductivity which is closest to the lowest possible value for the given geometry. / text