Multimode Analysis of Nanoscale Biomolecular Interactions

Biomolecular interactions, including protein-protein, protein-DNA, and protein-ligand interactions, are of special importance in all biological systems. These interactions may occer during the loading of biomolecules to interfaces, the translocation of biomolecules through transmembrane protein pores, and the movement of biomolecules in a crowded intracellular environment. The molecular interaction of a protein with its binding partners is crucial in fundamental biological processes such as electron transfer, intracellular signal transmission and regulation, neuroprotective mechanisms, and regulation of DNA topology. In this dissertation, a customized surface plasmon resonance (SPR) has been optimized and new theoretical and label free experimental methods with related analytical calculations have been developed for the analysis of biomolecular interactions. Human neuroglobin (hNgb) and cytochrome c from equine heart (Cyt c) proteins have been used to optimize the customized SPR instrument. The obtained Kd value (~13 µM), from SPR results, for Cyt c-hNgb molecular interactions is in general agreement with a previously published result. The SPR results also confirmed no significant impact of the internal disulfide bridge between Cys 46 and Cys 55 on hNgb binding to Cyt c. Using SPR, E. coli topoisomerase I enzyme turnover during plasmid DNA relaxation was found to be enhanced in the presence of Mg2+. In addition, a new theoretical approach of analyzing biphasic SPR data has been introduced based on analytical solutions of the biphasic rate equations. In order to develop a new label free method to quantitatively study protein-protein interactions, quartz nanopipettes were chemically modified. The derived Kd (~20 µM) value for the Cyt c-hNgb complex formations matched very well with SPR measurements (Kd ~16 µM). The finite element numerical simulation results were similar to the nanopipette experimental results. These results demonstrate that nanopipettes can potentially be used as a new class of a label-free analytical method to quantitatively characterize protein-protein interactions in attoliter sensing volumes, based on a charge sensing mechanism. Moreover, the molecule-based selective nature of hydrophobic and nanometer sized carbon nanotube (CNT) pores was observed. This result might be helpful to understand the selective nature of cellular transport through transmembrane protein pores.

Nano-grids of Yeast Cytochrome C

One innovative thought in biomolecular electronics is the exploitation of electron transfer proteins. Using nature's self assembly techniques, proteins can build highly organized edifices with retained functional activity, and they can serve as platforms for biosensors. In this research work, Yeast Cytochrome C (YCC) is immobilized with a help of a linker molecule, 3-Mercaptopropyltrimethoxysilane (3-MPTS) on a hydroxylated surface of a silicon substrate. Atomic Force Microscopy (AFM) is used for characterization. AFM data shows immobilization of one YCC molecule in between eight grids that are formed by the linker molecules. 3-MPTS monolayers are organized in grids that are 1.2 nm apart. Immobilization of 3-MPTS was optimized using a concentration of 5 mM in a completely dehydrated state for 30 minutes. The functionally active grids of YCC can now be incorporated with Cytochrome C oxidase on a Platinum electrode surface for transfer of electrons in development of biosensors, such as nitrate sensor, that are small in size, cheaper, and easier to manufacture than the top-down approach of fabrication of molecular biodevices

AFM and SPR studies of protein adsorption at solid/liquid interface

Membrane-like structure formed by surfactant molecules of didodecyldimethylammonium bromide (DDAB) on both HOPG and gold electrodes were studied with AFM and SPR techniques. The study shows that the thickness of the adsorbed layer of DDAB is strongly dependent on the concentration of the vesicle solution. We have also investigated the adsorption of redox protein, Cytochrome c, on graphite electrode with in situ tapping mode AFM. The protein adsorbs spontaneously onto the electrode covered with an adsorbed phosphate layer and forms a uniform monolayer. The adsorbed protein exhibits a reversible electron transfer at 0.17 V (Ag/AgCI) once the electrode potential has been increased to 0.75V. Using surface plasmon resonance spectroscopy we have measured subtle conformational change in protein, Cyt c, due to electron transfer of a single electron on MPA-coated gold electrode. The electron transfer induced change in the resonant angle is about 0.006 deg., which corresponds to ~ 0.2 A decreases in the thickness. This is consistent with that reduced state is more compact than the oxidized state.

C-MEMS Based Micro Enzymatic Biofuel Cells

Miniaturized, self-sufficient bioelectronics powered by unconventional micropower may lead to a new generation of implantable, wireless, minimally invasive medical devices, such as pacemakers, defibrillators, drug-delivering pumps, sensor transmitters, and neurostimulators. Studies have shown that micro-enzymatic biofuel cells (EBFCs) are among the most intuitive candidates for in vivo micropower. In the fisrt part of this thesis, the prototype design of an EBFC chip, having 3D intedigitated microelectrode arrays was proposed to obtain an optimum design of 3D microelectrode arrays for carbon microelectromechanical systems (C-MEMS) based EBFCs. A detailed modeling solving partial differential equations (PDEs) by finite element techniques has been developed on the effect of 1) dimensions of microelectrodes, 2) spatial arrangement of 3D microelectrode arrays, 3) geometry of microelectrode on the EBFC performance based on COMSOL Multiphysics. In the second part of this thesis, in order to investigate the performance of an EBFC, behavior of an EBFC chip performance inside an artery has been studied. COMSOL Multiphysics software has also been applied to analyze mass transport for different orientations of an EBFC chip inside a blood artery. Two orientations: horizontal position (HP) and vertical position (VP) have been analyzed. The third part of this thesis has been focused on experimental work towards high performance EBFC. This work has integrated graphene/enzyme onto three-dimensional (3D) micropillar arrays in order to obtain efficient enzyme immobilization, enhanced enzyme loading and facilitate direct electron transfer. The developed 3D graphene/enzyme network based EBFC generated a maximum power density of 136.3 μWcm-2 at 0.59 V, which is almost 7 times of the maximum power density of the bare 3D carbon micropillar arrays based EBFC. To further improve the EBFC performance, reduced graphene oxide (rGO)/carbon nanotubes (CNTs) has been integrated onto 3D mciropillar arrays to further increase EBFC performance in the fourth part of this thesisThe developed rGO/CNTs based EBFC generated twice the maximum power density of rGO based EBFC. Through a comparison of experimental and theoretical results, the cell performance efficiency is noted to be 67%.

Hydrogen(electron-deuteron) studies of the deuteron at high squared momentum transfer

A high resolution study of the quasielastic 2 H(e, e'p)n reaction was performed in Hall A at the Thomas Jefferson Accelerator Facility in Newport News, Virginia. The measurements were performed at a central momentum transfer of : q: ∼ 2400 MeV/c, and at a central energy transfer of ω ∼ 1500 MeV, a four momentum transfer Q2 = 3.5 (GeV/c)2, covering missing momenta from 0 to 0.5 GeV/c. The majority of the measurements were performed at Φ = 180° and a small set of measurements were done at Φ = 0°. The Hall A High Resolution Spectrometers (HRS) were used to detect coincident electrons and protons, respectively. Absolute 2H(e, e'p) n cross sections were obtained as a function of the recoiling neutron scattering angle with respect to [special characters omitted]. The experimental results were compared to a Plane Wave Impulse Approximation (PWIA) model and to a calculation that includes Final State Interaction (FSI) effects. Experimental 2H(e, e'p)n cross sections were determined with an estimated systematic uncertainty of 7%. The general features of the measured cross sections are reproduced by Glauber based calculations that take the motion of the bound nucleons into account (GEA). Final State Interactions (FSI) contributions were found to depend strongly on the angle of the recoiling neutron with respect to the momentum transfer and on the missing momentum. We found a systematic deviation of the theoretical prediction of about 30%. At small &thetas; nq (&thetas;nq < 60°) the theory overpredicts the cross section while at large &thetas; nq (&thetas;nq > 80°) the theory underestimates the cross sections. We observed an enhancement of the cross section, due to FSI, of about 240%, as compared to PWIA, for a missing momentum of 0.4 GeV/c at an angle of 75°. For missing momentum of 0.5 GeV/c the enhancement of the cross section due to the same FSI effects, was about 270%. This is in agreement with GEA. Standard Glauber calculations predict this large contribution to occur at an angle of 90°. Our results show that GEA better describes the 2H(e, e'p)n reaction.

An investigation into advertising's ability to foster favorable evaluations of brand extensions

Taking a respected brand name and placing it on a new product has become a popular strategy for leveraging the name's equity and goodwill. Current research has indicated that the success of doing so depends in part on the perceived “fit” between the core brand and the extension. When the name is extended to a closely related product category, consumers are very likely to transfer their favorable attitudes toward the core to the extension. However, as the perceived fit declines, this transfer becomes less likely. ^ This dissertation examined whether particular advertising tactics (e.g., using a common endorser or logo for the core and the extension) could enhance perceived fit between the core brand and its extension, thus leading to more favorable attitudes toward the extension than would otherwise occur. The sample was undergraduate students from universities in the southeast. The generating mechanism tested was that the transfer of associations between core brand and extension would enhance the overlap of associations between the core brand and the potential extension. ^ Research questions were analyzed using a 3 (levels of fit) x 3 (treatments) x 2 (replicate) experiment. The data analysis was conducted with repeated measures ANOVA's, UNIVARIATE ANOVA's, UNIVARIATE ANCOVA'S, and planned linear contrasts. ^ The results, except for the hypotheses on fit as a mediator of extension attitude, do not indicate that the presence of an endorser or brand mark closely aligned with the core brand enhanced perceived fit between core brand and extension. ^

Electroproduction of hyperons at low momentum transfer

A high resolution study of the H(e,e'K+)Λ,Σ 0 reaction was performed at Hall A, TJNAF as part of the hypernuclear experiment E94-107. One important ingredient to the measurement of the hypernuclear cross section is the elementary cross section for production of hyperons, Λ and Σ0. This reaction was studied using a hydrogen (i.e. a proton) target. Data were taken at very low Q2 (∼0.07 (GeV/c) 2) and W∼2.2 GeV. Kaons were detected along the direction of q, the momentum transferred by the incident electron (&thetas;CM∼6°). In addition, there are few data available regarding electroproduction of hyperons at low Q2 and &thetas;CM and the available theoretical models differ significantly in this kinematical region of W. The measurement of the elementary cross section was performed by scaling the Monte Carlo cross section (MCEEP) with the experimental-to-simulated yield ratio. The Monte Carlo cross section includes an experimental fit and extrapolation from the existing data for electroproduction of hyperons. Moreover, the estimated transverse component of the electroproduction cross section of H(e,e'K+)Λ was compared to the different predictions of the theoretical models and exisiting data curves for photoproductions of hyperons. None of the models fully describe the cross-section results over the entire angular range. Furthermore, measurements of the Σ 0/Λ production ratio were performed at &thetas; CM∼6°, where data are not available. Finally, data for the measurements of the differential cross sections and the Σ 0/Λ production were binned in Q2, W and &thetas;CM to understand the dependence on these variables. These results are not only a fundamental contribution to the hypernuclear spectroscopy studies but also an important experimental measurement to constrain existing theoretical models for the elementary reaction.

Electroproduction of hyperons at low momentum transfer

A high resolution study of the H(e,e'K+)Λ,Σ0 reaction was performed at Hall A, TJNAF as part of the hypernuclear experiment E94-107. One important ingredient to the measurement of the hypernuclear cross section is the elementary cross section for production of hyperons, Λ and Σ0. This reaction was studied using a hydrogen (i.e. a proton) target. Data were taken at very low Q2 (∼0.07 (GeV/c)2) and W∼2.2 GeV. Kaons were detected along the direction of q, the momentum transferred by the incident electron (θCM~6°). In addition, there are few data available regarding electroproduction of hyperons at low Q2 and θCM, and the available theoretical models differ significantly in this kinematical region of W. The measurement of the elementary cross section was performed by scaling the Monte Carlo cross section (MCEEP) with the experimental-to-simulated yield ratio. The Monte Carlo cross section includes an experimental fit and extrapolation from the existing data for electroproduction of hyperons. Moreover, the estimated transverse component of the electroproduction cross section of H(e,e'K+)Λ was compared to the different predictions of the theoretical models and exisiting data curves for photoproductions of hyperons. None of the models fully describe the cross-section results over the entire angular range. Furthermore, measurements of the Σ0/Λ production ratio were performed at θCM, where data are not available. Finally, data for the measurements of the differential cross sections and the Σ0/Λ production were binned in Q2, W and θCM to understand the dependence on these variables. These results are not only a fundamental contribution to the hypernuclear spectroscopy studies but also an important experimental measurement to constrain existing theoretical models for the elementary reaction.

Simulation and analysis of network traffic for efficient and reliable information transfer

With the growing commercial importance of the Internet and the development of new real-time, connection-oriented services like IP-telephony and electronic commerce resilience is becoming a key issue in the design of TP-based networks. Two emerging technologies, which can accomplish the task of efficient information transfer, are Multiprotocol Label Switching (MPLS) and Differentiated Services. A main benefit of MPLS is the ability to introduce traffic-engineering concepts due to its connection-oriented characteristic. With MPLS it is possible to assign different paths for packets through the network. Differentiated services divides traffic into different classes and treat them differently, especially when there is a shortage of network resources. In this thesis, a framework was proposed to integrate the above two technologies and its performance in providing load balancing and improving QoS was evaluated. Simulation and analysis of this framework demonstrated that the combination of MPLS and Differentiated services is a powerful tool for QoS provisioning in IP networks.