Growth, modification and integration of carbon nanotubes into molecular electronics

Molecules are the smallest possible elements for electronic devices, with active elements for such devices typically a few Angstroms in footprint area. Owing to the possibility of producing ultrahigh density devices, tremendous effort has been invested in producing electronic junctions by using various types of molecules. The major issues for molecular electronics include (1) developing an effective scheme to connect molecules with the present micro- and nano-technology, (2) increasing the lifetime and stabilities of the devices, and (3) increasing their performance in comparison to the state-of-the-art devices. In this work, we attempt to use carbon nanotubes (CNTs) as the interconnecting nanoelectrodes between molecules and microelectrodes. The ultimate goal is to use two individual CNTs to sandwich molecules in a cross-bar configuration while having these CNTs connected with microelectrodes such that the junction displays the electronic character of the molecule chosen. We have successfully developed an effective scheme to connect molecules with CNTs, which is scalable to arrays of molecular electronic devices. To realize this far reaching goal, the following technical topics have been investigated. 1. Synthesis of multi-walled carbon nanotubes (MWCNTs) by thermal chemical vapor deposition (T-CVD) and plasma-enhanced chemical vapor deposition (PECVD) techniques (Chapter 3). We have evaluated the potential use of tubular and bamboo-like MWCNTs grown by T-CVD and PE-CVD in terms of their structural properties. 2. Horizontal dispersion of MWCNTs with and without surfactants, and the integration of MWCNTs to microelectrodes using deposition by dielectrophoresis (DEP) (Chapter 4). We have systematically studied the use of surfactant molecules to disperse and horizontally align MWCNTs on substrates. In addition, DEP is shown to produce impurityfree placement of MWCNTs, forming connections between microelectrodes. We demonstrate the deposition density is tunable by both AC field strength and AC field frequency. 3. Etching of MWCNTs for the impurity-free nanoelectrodes (Chapter 5). We show that the residual Ni catalyst on MWCNTs can be removed by acid etching; the tip removal and collapsing of tubes into pyramids enhances the stability of field emission from the tube arrays. The acid-etching process can be used to functionalize the MWCNTs, which was used to make our initial CNT-nanoelectrode glucose sensors. Finally, lessons learned trying to perform spectroscopic analysis of the functionalized MWCNTs were vital for designing our final devices. 4. Molecular junction design and electrochemical synthesis of biphenyl molecules on carbon microelectrodes for all-carbon molecular devices (Chapter 6). Utilizing the experience gained on the work done so far, our final device design is described. We demonstrate the capability of preparing patterned glassy carbon films to serve as the bottom electrode in the new geometry. However, the molecular switching behavior of biphenyl was not observed by scanning tunneling microscopy (STM), mercury drop or fabricated glassy carbon/biphenyl/MWCNT junctions. Either the density of these molecules is not optimum for effective integration of devices using MWCNTs as the nanoelectrodes, or an electroactive contaminant was reduced instead of the ionic biphenyl species. 5. Self-assembly of octadecanethiol (ODT) molecules on gold microelectrodes for functional molecular devices (Chapter 7). We have realized an effective scheme to produce Au/ODT/MWCNT junctions by spanning MWCNTs across ODT-functionalized microelectrodes. A percentage of the resulting junctions retain the expected character of an ODT monolayer. While the process is not yet optimized, our successful junctions show that molecular electronic devices can be fabricated using simple processes such as photolithography, self-assembled monolayers and dielectrophoresis.

Measuring energy spectra of TeV gamma-ray emission from the Cygnus region of our galaxy with Milagro

High energy gamma rays can provide fundamental clues to the origins of cosmic rays. In this thesis, TeV gamma-ray emission from the Cygnus region is studied. Previously the Milagro experiment detected five TeV gamma-ray sources in this region and a significant excess of TeV gamma rays whose origin is still unclear. To better understand the diffuse excess the separation of sources and diffuse emission is studied using the latest and most sensitive data set of the Milagro experiment. In addition, a newly developed technique is applied that allows the energy spectrum of the TeV gamma rays to be reconstructed using Milagro data. No conclusive statement can be made about the spectrum of the diffuse emission from the Cygnus region because of its low significance of 2.2 σ above the background in the studied data sample. The entire Cygnus region emission is best fit with a power law with a spectral index of α=2.40 (68% confidence interval: 1.35-2.92) and a exponential cutoff energy of 31.6 TeV (10.0-251.2 TeV). In the case of a simple power law assumption without a cutoff energy the best fit yields a spectral index of α=2.97 (68% confidence interval: 2.83-3.10). Neither of these best fits are in good agreement with the data. The best spectral fit to the TeV emission from MGRO J2019+37, the brightest source in the Cygnus region, yields a spectral index of α=2.30 (68% confidence interval: 1.40-2.70) with a cutoff energy of 50.1 TeV (68% confidence interval: 17.8-251.2 TeV) and a spectral index of α=2.75 (68% confidence interval: 2.65-2.85) when no exponential cutoff energy is assumed. According to the present analysis, MGRO J2019+37 contributes 25% to the differential flux from the entire Cygnus at 15 TeV.

Charge and spin transport in nanoscale junction from first principles

Recently nanoscale junctions consisting of 0-D nanostructures (single molecule) or 1-D nanostructures (semiconducting nanowire) sandwiched between two metal electrodes are successfully fabricated and characterized. What lacks in the recent developments is the understanding of the mechanism behind the observed phenomena at the level of atoms and electrons. For example, the origin of observed switching effect in a semiconducting nanowire due to the influence of an external gate bias is not yet understood at the electronic structure level. On the same context, different experimental groups have reported different signs in tunneling magneto-resistance for the same organic spin valve structure, which has baffled researchers working in this field. In this thesis, we present the answers to some of these subtle questions by investigating the charge and spin transport in different nanoscale junctions. A parameter-free, single particle Green’s function approach in conjunction with a posteriori density functional theory (DFT) involving a hybrid orbital dependent functional is used to calculate the tunneling current in the coherent transport limit. The effect of spin polarization is explicitly incorporated to investigate spin transport in a nanoscale junction. Through the electron transport studies in PbS nanowire junction, a new orbital controlled mechanism behind the switching of the current is proposed. It can explain the switching behavior, not only in PbS nanowire, but in other lead-chalcogenide nanowires as well. Beside this, the electronic structure properties of this nanowire are studied using periodic DFT. The quantum confinement effect was investigated by calculating the bandgap of PbS nanowires with different diameters. Subsequently, we explain an observed semiconducting to metallic phase transition of this nanowire by calculating the bandgap of the nanowire under uniform radial strain. The compressive radial strain on the nanowire was found to be responsible for the metallic to semiconducting phase transition. Apart from studying one dimensional nanostructure, we also present transport properties in zero dimensional single molecular junctions. We proposed a new codoping approach in a single molecular carborane junction, where a cation and an anion are simultaneously doped to find the role of a single atom in the device. The main purpose was to build a molecular junction where a single atom can dictate the flow of electrons in a circuit. Recent observations of both positive and negative sign in tunneling magnetoresistance (TMR) the using same organic spin-valve structure hasmystified researchers. From our spin dependent transport studies in a prototypical organic molecular tunneling device, we found that a 3% change in metal-molecule interfacial distance can alter the sign of TMR. Changing the interfacial distance by 3%, the number of participating eigenstates as well as their orbital characteristic changes for anti-parallel configuration of the magnetization at the two electrodes, leading to the sign reversal of the TMR. Apart from this, the magnetic proximity effect under applied bias is investigated quantitatively, which can be used to understand the observed unexpectedmagnetismin carbon basedmaterials when they are in close proximity with magnetic substrates.

Controlling electronic and magnetic properties of ultra narrow multilayered nanowires

Interest in the study of magnetic/non-magnetic multilayered structures took a giant leap since Grünberg and his group established that the interlayer exchange coupling (IEC) is a function of the non-magnetic spacer width. This interest was further fuelled by the discovery of the phenomenal Giant Magnetoresistance (GMR) effect. In fact, in 2007 Albert Fert and Peter Grünberg were awarded the Nobel Prize in Physics for their contribution to the discovery of GMR. GMR is the key property that is being used in the read-head of the present day computer hard drive as it requires a high sensitivity in the detection of magnetic field. The recent increase in demand for device miniaturization encouraged researchers to look for GMR in nanoscale multilayered structures. In this context, one dimensional(1-D) multilayerd nanowire structure has shown tremendous promise as a viable candidate for ultra sensitive read head sensors. In fact, the phenomenal giant magnetoresistance(GMR) effect, which is the novel feature of the currently used multilayered thin film, has already been observed in multilayered nanowire systems at ambient temperature. Geometrical confinement of the supper lattice along the 2-dimensions (2-D) to construct the 1-D multilayered nanowire prohibits the minimization of magnetic interaction- offering a rich variety of magnetic properties in nanowire that can be exploited for novel functionality. In addition, introduction of non-magnetic spacer between the magnetic layers presents additional advantage in controlling magnetic properties via tuning the interlayer magnetic interaction. Despite of a large volume of theoretical works devoted towards the understanding of GMR and IEC in super lattice structures, limited theoretical calculations are reported in 1-D multilayered systems. Thus to gauge their potential application in new generation magneto-electronic devices, in this thesis, I have discussed the usage of first principles density functional theory (DFT) in predicting the equilibrium structure, stability as well as electronic and magnetic properties of one dimensional multilayered nanowires. Particularly, I have focused on the electronic and magnetic properties of Fe/Pt multilayered nanowire structures and the role of non-magnetic Pt spacer in modulating the magnetic properties of the wire. It is found that the average magnetic moment per atom in the nanowire increases monotonically with an ~1/(N(Fe)) dependance, where N(Fe) is the number of iron layers in the nanowire. A simple model based upon the interfacial structure is given to explain the 1/(N(Fe)) trend in magnetic moment obtained from the first principle calculations. A new mechanism, based upon spin flip with in the layer and multistep electron transfer between the layers, is proposed to elucidate the enhancement of magnetic moment of Iron atom at the Platinum interface. The calculated IEC in the Fe/Pt multilayered nanowire is found to switch sign as the width of the non-magnetic spacer varies. The competition among short and long range direct exchange and the super exchange has been found to play a key role for the non-monotonous sign in IEC depending upon the width of the Platinum spacer layer. The calculated magnetoresistance from Julliere's model also exhibit similar switching behavior as that of IEC. The universality of the behavior of exchange coupling has also been looked into by introducing different non-magnetic spacers like Palladium, Copper, Silver, and Gold in between magnetic Iron layers. The nature of hybridization between Fe and other non-magnetic spacer is found to dictate the inter layer magnetic interaction. For example, in Fe/Pd nanowire the d-p hybridization in two spacer layer case favors anti-ferromagnetic (AFM) configuration over ferromagnetic (FM) configuration. However, the hybridization between half-filled Fe(d) and filled Cu(p) state in Fe/Cu nanowire favors FM coupling in the 2-spacer system.

Calibration of the HAWC Gamma-Ray Observatory

The High-Altitude Water Cherenkov (HAWC) Experiment is a gamma-ray observatory that utilizes water silos as Cherenkov detectors to measure the electromagnetic air showers created by gamma rays. The experiment consists of an array of closely packed water Cherenkov detectors (WCDs), each with four photomultiplier tubes (PMTs). The direction of the gamma ray will be reconstructed using the times when the electromagnetic shower front triggers PMTs in each WCD. To achieve an angular resolution as low as 0.1 degrees, a laser calibration system will be used to measure relative PMT response times. The system will direct 300ps laser pulses into two fiber-optic networks. Each network will use optical fan-outs and switches to direct light to specific WCDs. The first network is used to measure the light transit time out to each pair of detectors, and the second network sends light to each detector, calibrating the response times of the four PMTs within each detector. As the relative PMT response times are dependent on the number of photons in the light pulse, neutral density filters will be used to control the light intensity across five orders of magnitude. This system will run both continuously in a low-rate mode, and in a high-rate mode with many intensity levels. In this thesis, the design of the calibration system and systematic studies verifying its performance are presented.

Characterizing a single photon detector

I will present my work about constructing and characterizing a single photon detector. Using the 1550nm laser and second harmonic light generation, I am able to count single photons on a Multi‐Pixel Photon Counter (MPPC) silicon APD. My results show that upwards of 22% quantum efficiency is achievable with the MPPC. Future work will include coincidence detection of correlated photon‐pair.

Planar magneto-photonic and gradient-photonic structures : crystals and metamaterials.

In the field of photonics, two new types of material structures, photonic crystals and metamaterials, are presently of great interest. Both are studied in the present work, which focus on planar magnetic materials in the former and planar gradient metamaterials in the latter. These planar periodic structures are easy to handle and integrate into optical systems. The applications are promising field for future optical telecommunication systems and give rise to new optical, microwave and radio technologies. The photonic crystal part emphasizes the utilization of magnetic material based photonic crystals due to its remarkable magneto-optical characteristics. Bandgaps tuning by magnetic field in bismuth-gadolinium-substituted lutetium iron garnet (Bi0.8 Gd0.2 Lu2.0 Fe5 O12) based one- dimensional photonic crystals are investigated and demonstrated in this work. Magnetic optical switches are fabricated and tested. Waveguide formulation for band structure in magneto photonic crystals is developed. We also for the first time demonstrate and test two- dimensional magneto photonic crystals optical. We observe multi-stopbands in two- dimensional photonic waveguide system and study the origin of multi-stopbands. The second part focus on studying photonic metamaterials and planar gradient photonic metamaterial design. We systematically study the effects of varying the geometry of the fishnet unit cell on the refractive index in optical frequency. It is the first time to design and demonstrate the planar gradient structure in the high optical frequency. Optical beam bending using planar gradient photonic metamaterials is observed. The technologies needed for the fabrication of the planar gradient photonic metamaterials are investigated. Beam steering devices, shifter, gradient optical lenses and etc. can be derived from this design.

Electronic properties of zig-zag carbon nanotubes : a first-principles study

Carbon nanotube (CNT) is a one dimensional (1-D) nanostructured material, which has been the focal point of research over the past decade for intriguing applications ranging from nanoelectronics to chemical and biological sensors. Using a first-principles gradient corrected density functional approach, we present a comprehensive study of the geometry and energy band gap in zig-zag semi-conducting (n,0) carbon nanotubes (CNT) to resolve some of the conflicting findings. Our calculations confirm that the single wall (n,0) CNTs fall into two distinct classes depending upon n mod 3 equal to 1 (smaller band gaps) or 2 (larger gaps). The effect of longitudinal strain on the band gap further confirms the existence of two distinct classes: for n mod 3 = 1 or 2, changing Eg by ~ ±110 meV for 1% strain in each case. We also present our findings for the origin of metallicity in multiwall CNTs.

Four-window technique for measuring optical-phase-space-time-frequency tomography

A new approach, the four-window technique, was developed to measure optical phase-space-time-frequency tomography (OPSTFT). The four-window technique is based on balanced heterodyne detection with two local oscillator (LO) fields. This technique can provide independent control of position, momentum, time and frequency resolution. The OPSTFT is a Wigner distribution function of two independent Fourier transform pairs, phase-space and time-frequency. The OPSTFT can be applied for early disease detection.

Quantum transport in a single molecular junction

The craze for faster and smaller electronic devices has never gone down and this has always kept researchers on their toes. Following Moore’s law, which states that the number of transistors in a single chip will double in every 18 months, today “30 million transistors can fit into the head of a 1.5 mm diameter pin”. But this miniaturization cannot continue indefinitely due to the ‘quantum leakage’ limit in the thickness of the insulating layer between the gate electrode and the current carrying channel. To bypass this limitation, scientists came up with the idea of using vastly available organic molecules as components in an electronic device. One of the primary challenges in this field was the ability to perform conductance measurements across single molecular junctions. Once that was achieved the focus shifted to a deeper understanding of the underlying physics behind the electron transport across these molecular scale devices. Our initial theoretical approach is based on the conventional Non-Equilibrium Green Function(NEGF) formulation, but the self-energy of the leads is modified to include a weighting factor that ensures negligible current in the absence of a molecular pathway as observed in a Mechanically Controlled Break Junction (MCBJ) experiment. The formulation is then made parameter free by a more careful estimation of the self-energy of the leads. The calculated conductance turns out to be atleast an order more than the experimental values which is probably due to a strong chemical bond at the metal-molecule junction unlike in the experiments. The focus is then shifted to a comparative study of charge transport in molecular wires of different lengths within the same formalism. The molecular wires, composed of a series of organic molecules, are sanwiched between two gold electrodes to make a two terminal device. The length of the wire is increased by sequentially increasing the number of molecules in the wire from 1 to 3. In the low bias regime all the molecular devices are found to exhibit Ohmic behavior. However, the magnitude of conductance decreases exponentially with increase in length of the wire. In the next study, the relative contribution of the ‘in-phase’ and the ‘out-of-phase’ components of the total electronic current under the influence of an external bias is estimated for the wires of three different lengths. In the low bias regime, the ‘out-of-phase’ contribution to the total current is minimal and the ‘in-phase’ elastic tunneling of the electrons is responsible for the net electronic current. This is true irrespective of the length of the molecular spacer. In this regime, the current-voltage characteristics follow Ohm’s law and the conductance of the wires is found to decrease exponentially with increase in length which is in agreement with experimental results. However, after a certain ‘off-set’ voltage, the current increases non-linearly with bias and the ‘out-of-phase’ tunneling of electrons reduces the net current substantially. Subsequently, the interaction of conduction electrons with the vibrational modes as a function of external bias in the three different oligomers is studied since they are one of the main sources of phase-breaking scattering. The number of vibrational modes that couple strongly with the frontier molecular orbitals are found to increase with length of the spacer and the external field. This is consistent with the existence of lowest ‘off-set’ voltage for the longest wire under study.

First-principles studies of boron nanostructures

Boron is an 'electron deficient' element which has a rather fascinating chemical versatility. In the solid state, the elemental boron has neither a pure covalent nor a pure metallic character. As a result, its vast structural dimensionally and peculiar bonding features hold a unique place among other elements in the periodic table. In order to understand and properly describe these unusual bonding features, a detailed and systematic theoretical study is needed. In this work, I will show that some of the qualitative features of boron nanostructures, including clusters, sheets and nanotubes can easily be extracted from the results of first principles calculations based on density functional theory. Specifically, the size-dependent evolution of topological structures and bonding characteristics of boron clusters, Bn will be discussed. Based on the scenario observed in the boron clusters, the unique properties of boron sheets and boron nanotubes will be described. Moreover, the ballistic electron transport in single-walled carbon nanotubes will be considered. It is expected that the theoretical results obtained in the present thesis will initiate further studies on boron nanostructures, which will be helpful in understanding, designing and realizing boron-based nanoscale devices.

Studies of spatial clustering of inertial particles in turbulence

We present studies of the spatial clustering of inertial particles embedded in turbulent flow. A major part of the thesis is experimental, involving the technique of Phase Doppler Interferometry (PDI). The thesis also includes significant amount of simulation studies and some theoretical considerations. We describe the details of PDI and explain why it is suitable for study of particle clustering in turbulent flow with a strong mean velocity. We introduce the concept of the radial distribution function (RDF) as our chosen way of quantifying inertial particle clustering and present some original works on foundational and practical considerations related to it. These include methods of treating finite sampling size, interpretation of the magnitude of RDF and the possibility of isolating RDF signature of inertial clustering from that of large scale mixing. In experimental work, we used the PDI to observe clustering of water droplets in a turbulent wind tunnel. From that we present, in the form of a published paper, evidence of dynamical similarity (Stokes number similarity) of inertial particle clustering together with other results in qualitative agreement with available theoretical prediction and simulation results. We next show detailed quantitative comparisons of results from our experiments, direct-numerical-simulation (DNS) and theory. Very promising agreement was found for like-sized particles (mono-disperse). Theory is found to be incorrect regarding clustering of different-sized particles and we propose a empirical correction based on the DNS and experimental results. Besides this, we also discovered a few interesting characteristics of inertial clustering. Firstly, through observations, we found an intriguing possibility for modeling the RDF arising from inertial clustering that has only one (sensitive) parameter. We also found that clustering becomes saturated at high Reynolds number.

PMMA-CNT matrices for vacuum electronic, biosensing and energy applications

Carbon nanotubes (CNTs) are interesting materials with extraordinary properties for various applications. Here, vertically-aligned multiwalled CNTs (VA-MWCNTs) are grown by our dual radio frequency plasma enhanced chemical vapor deposition (PECVD). After optimizing the synthesis processes, these VA-MWCNTs were fabricated in to a series of devices for applications in vacuum electronics, glucose biosensors, glucose biofuel cells, and supercapacitors In particular, we have created the so-called PMMA-CNT matrices (opened-tip CNTs embedded in poly-methyl methacrylate) that are promising components in a novel energy sensing, generation and storage (SGS) system that integrate glucose biosensors, biofuel cells, and supercapacitors. The content of this thesis work is described as follows: 1. We have first optimized the synthesis of VA-MWCNTs by our PECVD technique. The effects of CH4 flow rate and growth duration on the lengths of these CNTs were studied. 2. We have characterized these VA-MWCNTs for electron field emission. We noticed that as grown CNTs suffers from high emission threshold, poor emission density and poor long-term stability. We attempted a series of experiments to understand ways to overcome these problems. First, we decrease the screening effects on VA-MWCNTs by creating arrays of self-assembled CNT bundles that are catalyst-free and opened tips. These bundles are found to enhance the field emission stability and emission density. Subsequently, we have created PMMA-CNT matrices that are excellent electron field emitters with an emission threshold field of more than two-fold lower than that of the as-grown sample. Furthermore, no significant emission degradation was observed after a continuous emission test of 40 hours (versus much shorter tests in reported literatures). Based on the new understanding we learnt from the PMMA-CNT matrices, we further created PMMA-STO-CNT matrices by embedding opened-tip VA-MWCNTs that are coated with strontium titanate (SrTiO3) with PMMA. We found that the PMMA-STO-CNT matrices have all the desired properties of the PMMA-CNT matrices. Furthermore, PMMA-STO-CNT matrices offer much lower emission threshold field, about five-fold lower than that of as grown VA-MWCNTs. The new understandings we obtained are important for practical application of VA-MWCNTs in field emission devices. 3. Subsequently, we have functionalized PMMA-CNT matrices for glucose biosensing. Our biosensor was developed by immobilized glucose oxidase (GOχ) on the opened-tip CNTs exposed on the matrices. The durability, stability and sensitivity of the biosensor were studied. In order to understand the performance of miniaturized glucose biosensors, we have then investigated the effect of working electrode area on the sensitivity and current level of our biosensors. 4. Next, functionalized PMMA-CNT matrices were utilized for energy generation and storage. We found that PMMA-CNT matrices are promising component in glucose/O2 biofuel cells (BFCs) for energy generation. The construction of these BFCs and the effect of the electrode area on the power density of these BFCs were investigated. Then, we have attempted to use PMMA-CNT matrices as supercapacitors for energy storage devices. The performance of these supercapacitors and ways to enhance their performance are discussed. 5. Finally, we further evaluated the concept of energy SGS system that integrated glucose biosensors, biofuel cells, and supercapacitors. This SGS system may be implantable to monitor and control the blood glucose level in our body.

Proteins in silico-modeling and sampling

Proteins are linear chain molecules made out of amino acids. Only when they fold to their native states, they become functional. This dissertation aims to model the solvent (environment) effect and to develop & implement enhanced sampling methods that enable a reliable study of the protein folding problem in silico. We have developed an enhanced solvation model based on the solution to the Poisson-Boltzmann equation in order to describe the solvent effect. Following the quantum mechanical Polarizable Continuum Model (PCM), we decomposed net solvation free energy into three physical terms– Polarization, Dispersion and Cavitation. All the terms were implemented, analyzed and parametrized individually to obtain a high level of accuracy. In order to describe the thermodynamics of proteins, their conformational space needs to be sampled thoroughly. Simulations of proteins are hampered by slow relaxation due to their rugged free-energy landscape, with the barriers between minima being higher than the thermal energy at physiological temperatures. In order to overcome this problem a number of approaches have been proposed of which replica exchange method (REM) is the most popular. In this dissertation we describe a new variant of canonical replica exchange method in the context of molecular dynamic simulation. The advantage of this new method is the easily tunable high acceptance rate for the replica exchange. We call our method Microcanonical Replica Exchange Molecular Dynamic (MREMD). We have described the theoretical frame work, comment on its actual implementation, and its application to Trp-cage mini-protein in implicit solvent. We have been able to correctly predict the folding thermodynamics of this protein using our approach.