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The rational design, synthesis, and characterization of several systems that undergo self-assembly are described. Systems were chosen based on their ability to self-assemble in a highly ordered and predictable fashion that imparts order on the structure such that it is able to perform a given device function. Herein we describe self-assembled multilayered thin films on gold that can behave as molecular wires with tunable length, photocurrent generating films, and surfaces with photoswitchable wettability, and self-assembling peptide nanotubes that can potentially function as long range energy and electron transfer conduits. A non-covalent, modular approach to multilayered thin film fabrication was used to generate three thin film systems that function as molecular scale wires, photocurrent generating devices, and photoswitchable thin films, respectively. These films were based on 4-[(10-mercaptodecyl)oxy]pyridine-2,6-dicarboxylic acid self-assembled monolayers on gold. These monolayers are able to chelate metal (II) ions, and thus multilayers were assembled based on metal-ligand coordination chemistry. The three systems described were characterized by contact angle measurements, electrochemical methods, and grazing angle IR spectroscopy. All three systems emphasize the versatility of a modular approach to thin film construction, and provide proof-of-concept for future studies. A cyclic octapeptide architecture was employed as a scaffold for the predictable self-assembly of photoactive groups within a nanotubular structure. The degree of cyclic peptide aggregation in stacking nanotube systems and non-stacking monomer systems, was studied via fluorescence emission spectroscopy. Based on the spectral results, it was determined that peptide nanotubes can be constructed such that photoactive side chains can be assembled in stacks. Future experiments for the determination of long range energy and/or charge transfer in these systems are also discussed.

"Self-assembled monolayers (SAMs) are organized molecular assemblies that are formed by spontaneous adsorption of a compound in solution to a surface (e.g. alkanethiols on gold). The design, preparation, and characterization of several self-assembled monolayers and multilayers on surfaces (gold, indium tin oxide and quartz) are described. The systems were chosen based on their ability to form ordered films and to perform a given device function. SAMs were fabricated with selected functional groups at the air-monolayer interface, capable of complexing metal ions (e.g. dicarboxypyridine, dicarboxybenzene, imidazole, 4-hydroxypyridine) with the purpose of using these SAMs to construct multilayered films. Deposition of a second layer consisting of metal ions (e.g. Cu(II), Co(II) and Fe(III)), occurs by non-covalent metal ligand binding interactions between the metal ion layer and the different organic ligands on the surface. Deposition of subsequent layers was achieved by the incorporation of the appropriate organic ligands and metal ions. These monolayers and multilayered films were characterized by contact angle measurements, ellipsometry, grazing angle FT-IR, cyclic voltammetry and impedance spectroscopy following deposition of each layer on the film. Electrochemical analysis of the multilayered films shows alternating insulating/conducting behavior (cyclic voltammetry) and alternating changes in films capacitance (impedance spectroscopy) depending on the outermost layer of the film. Films capped with an organic layer show low conductivity, while films capped with a metal layer show conducting behavior. The electrochemical behavior of the films is related to the degree of “leakiness” or electrolyte solution permeation through the film, which is high for films with metal layers as the top layer and decreases once the film is capped with an organic layer. The alternating conducting/insulating behavior of the films allows for fabrication of multilayered thin films of variable thickness and tunable conducting properties. Ordered films were fabricated with up to seven layers of dicarboxypyridine and Cu(II), and 4-hydroxypyridine and Fe(III) metal-ligand units. The construction of these films provides an example of molecular films that could function as molecular wires or junctions due to their controllable electrochemical properties. Photocurrent generating films were fabricated by incorporation of chromophore groups (e.g. pyrene, porphyrins) into the multilayered structures. These films generate cathodic or anodic current upon photoexcitation of the chromophores. The monolayers functionalized with different organic ligands were also used to study lanthanide complexation on the surfaces. Successful deposition of different lanthanide ions was achieved from DMSO solutions. Monolayers of a bicyclic structure, 4, 7, 13, 16-tetraoxa-1,10,21-triaza-bicycle[8.8.5] tricosane-19,23-dione, attached to a hexadecanethiol molecule were used to study the ability of metal ion detection on the surface using electrochemical (cyclic voltammetry and impedance spectroscopy) techniques. The SAMs show higher complexation affinity for Li+ than for Na+ or K+. Preliminary studies were also carried out to investigate the ability of different SAMs to cell adhesion interactions. Future experiments will help elucidate a systematic relation of cell adherence and the bulk and molecular-level properties of the functionalized surfaces. The different multilayered films described in this dissertation served as preliminary models for different molecular scale device applications. Current work is focused in the design and preparation of more efficient photocurrent generating films, highly selective sensors for different types of ions, surfaces for cell adhesion and microbial interactions, and the study of other potential applications such as the design of micro and nanofluidic devices. "

Nano-materials are interesting material category with a single unit size between 1 and 1000 nanometers and possess unique mechanical, electrical, optical, and other physical properties that make them stand out from ordinary materials. With increasing demand for reduced size of electronic devices and integrated micro/nano-electro-mechanical systems (MEMS / NEMS), there is a high driving force in scientific research and technological advancement in nanotechnology. My research is about two popular novel nanomaterials: carbon nanotubes (1-dimensional material) and thin-layer transition metal dichalcogenides (2-dimensional materials). My first research direction is about the characterization of electrical properties of carbon nanotubes and using them as bio-sensors. Carbon nanotubes (CNTs), in general, are a material of great interest for many applications since their first discovery in 1991 [1], due to their unique structure, extraordinary electrical and mechanical properties, and unusual chemical properties. High-throughput fabrication of carbon nanotube field effect transistors (CNTFETs) with uniform properties has been a challenge since they were first fabricated in 1998. We invent a novel fabrication method to produce a 1×1 cm2 chip with over 700 CNTFETs fabricated around one single carbon nanotube. This large number of devices allows us to study the stability and uniformity of CNTFET properties. We grow flow-aligned CNTs on a SiO2/Si substrate by chemical vapor deposition and locate a single long CNT (as long as 1 cm) by scanning electron microscopy. Two photolithography steps are then used, first to pattern contacts and bonding pads, and next to define a mask to ‘burn’ away additional nanotubes by oxygen plasma etch. A fabrication yield of ~72% is achieved. The authors present statistics of the transport properties of these devices, which indicates that all the CNTFETs share the same threshold voltage, and similar on-state conductance. These devices are then used to measure DNA conductance by connecting DNA molecule of varying lengths to lithographically cut CNTFETs. While one single carbon nanotube is considered 1-dimensional material because it only has one side with “non-nano” length, the thin-layer transition metal dichalcogenides (TMDCs) are called the 2-dimensional materials since they have two sides of normal lengths and the other side of atomic size. Atomically thin materials such as graphene and semiconducting transition metal dichalcogenides have attracted extensive interests in recent years, motivating investigation into multiple properties. We use a refined version of the optothermal Raman technique [2][3] to measure the thermal transport properties of two TMDC materials, MoS2 and MoSe2, in single-layer (1L) and bi-layer (2L) forms. This new version incorporates two crucial improvements over previous implementations. First, we utilize more direct measurements of the optical absorption of the suspended samples under study and find values ~40% lower than previously assumed. Second, by comparing the response of fully supported and suspended samples using different laser spot sizes, we are able to independently measure the interfacial thermal conductance to the substrate and the lateral thermal conductivity of the supported and suspended materials. The approach is validated by examining the response of a suspended film illuminated in different positions in radial direction. For 1L MoS2 and MoSe2, the room-temperature thermal conductivities are (80±17) W/mK and (55±18) W/mK, respectively. For 2L MoS2 and MoSe2, we obtain values of (73±25) W/mK and (39±13) W/mK. Crucially, the interfacial thermal conductance is found to be of order 0.1-1 MW/m2K, substantially smaller than previously assumed, a finding that has important implications for design and modeling of electronic devices.

MoS2, among many other transition metal dichalcogenides (TMDCs), holds great promise for future applications in nano-electronics, opto-electronics and mechanical devices due to its ultra-thin nature, flexibility, sizable band-gap, and unique spin-valley coupled physics. However, there are two main challenges that hinder careful study of this material. Firstly, it is hard to achieve Ohmic contacts to mono-layer MoS2, particularly at low temperatures (T) and low carrier densities. Secondly, materials' low quality and impurities introduced during the fabrication significantly limit the electron mobility of mono- and few-layer MoS2 to be substantially below theoretically predicted limits, which has hampered efforts to observe its novel quantum transport behaviours. Traditional low work function metals doesn't necessary provide good electron injection to thin MoS2 due to metal oxidation, Fermi level pinning, etc. To address the first challenge, we tried multiple contact schemes and found that mono-layer hexagonal boron nitride (h-BN) and cobalt (Co) provide robust Ohmic contact. The mono-layer spacer serves two advantageous purposes: it strongly interacts with the transition metal, reducing its work function by over 1 eV; and breaks the metal-TMDCs interaction to eliminate the interfacial states that cause Fermi level pinning. We measure a flat-band Schottky barrier of 16 meV, which makes thin tunnel barriers upon doping the channels, and thus achieve low-T contact resistance of 3 kohm.um at a carrier density of 5.3x10^12/cm^2. Similar to graphene, eliminating all potential sources of disorder and scattering is the key to achieving high performance in MoS2 devices. We developed a van der Waals heterostructure device platform where MoS2 layers are fully encapsulated within h-BN and electrically contacted in a multi-terminal geometry using gate-tunable graphene electrodes. The h-BN-encapsulation provides excellent protection from environmental factors, resulting in highly stable device performance, even at elevated temperatures. Both optical and electrical characterization confirms our high quality devices, including an ultra-clean interface, a record-high Hall mobility reaching 34,000 cm^2/Vs, and first observation of Shubnikov–de Haas oscillations. The development of Ohmic contact and fabrication of high quality devices are critical to MoS2 application and studying its intrinsic properties. Therefore, the progress made in this work will facilitate efforts to study novel physical phenomena of MoS2 that were not accessible before.

In the last 50 years, the semiconductor industry has been scaling the silicon transistor to achieve faster devices, lower power consumption, and improve device performance. Transistor gate dimensions have become so small that short channel effects and gate leakage have become a significant problem. To address these issues, performance enhancement techniques such as strained silicon are used to improve mobility, while new high-k gate dielectric materials replace silicon oxide to reduce gate leakage. At some point the fundamental limit of silicon will be reached and the semiconductor industry will need to find an alternate solution. The advent of graphene led to the discovery of other layered materials such as the transition metal dichalcogenides. These materials have a layered structure similar to graphene and therefore possess some of the same qualities, but unlike graphene, these materials possess sizeable bandgaps between 1-2 eV making them useful for digital electronic applications. Since initially discovered, most of the research on these films has been from mechanically exfoliated flakes, which are easily produced due to the weak van der Waals force binding the layers together. For these materials to be considered for use in mainstream semiconductor technology, methods need to be explored to grow these films uniformly over a large area. In this research, atomic layer deposition (ALD) was employed as the growth technique used to produce large area uniform thin films of several different transition metal dichalcogenides. By optimizing the ALD growth parameters, it is possible to grow high quality films a few to several monolayers thick over a large area with good uniformity. This has been demonstrated and verified using several physical analytical tests such as Raman spectroscopy, photoluminescence, x-ray photoelectron spectroscopy, x-ray diffraction, transmission electron spectroscopy, and scanning electron microscopy, which show that these films possess the same qualities as those of the mechanically exfoliated films. Back-gated field effect transistors were created and electrical characterization was performed to determine if ALD grown films possess the same electronic properties as films produced from other methods. The tests revealed that the ALD grown films have high field effect mobility and high current on/off ratios. The WSe2 films also exhibited ambipolar electrical behavior making them a possible candidate for complementary metal-oxide semiconductor (CMOS) technology. Ab-initio density functional theory calculations were performed and compared to experimental properties of MoS2 and WSe2 films, which show that the ALD films grown in this research match theoretical predictions. The transconductance measurements from the WSe2 devices used, matched very well with the theoretical calculations, bridging the gap between experimental data and theoretical predictions. Based upon this research, ALD growth of TMD films proves to be a viable alternative for silicon based digital electronics.

The road map of the semiconductor industry has followed Moores Law over the past few decades. According to Moores Law the number of transistors in an integrated circuit (IC) will double for a minimum component cost every two years. The features made in an IC are produced by photolithography. Industry is now producing devices at the 65 nm node, however, for every deceasing node size, both the materials and processes used are not only difficult but also expensive to develop. Ultimately, the feature size obtainable via photolithography is dependent on the wavelength used in the process. The limitations of photolithography will eventually make Moores Law unsustainable. Therefore, new methodologies of creating features in the semiconductor substrate are desired. Here we present a new way to make patterns in silicon (Si) and silicon dioxide (SiO2), molecular lithography. Individual molecules and polymers, in a monolayer, serves directly as the etch mask; eliminating the photolighographic size limitation of light at a specific wavelength. The Ohnishi- and Ring parameter suggests that cyclic carbon rich molecules have a high resistance towards the plasma process, used to create the features in the substrate. Therefore highly aromatic molecules were investigated as candidates for molecular lithography. A monolayer of poly cyclic hydrocarbons, fullerene containing polymer, and fullerene molecules were created using the versatile photochemistry of benzophenone as the linker between the substrate and the material. First, a chlorosilane benzophenone derivative was attached to the Si/SiO2 surface. A thin film of the desired material is then created on top of the silane benzophenone layer. Irradiation at ~350 nm excites the benzophenone and reacts with neighboring alkyl chains. After covalent attachment the non-bonded molecules are extracted from the surface using a Soxhlet apparatus. Self-assembly, molecular weight, and wetting properties of the material dictates the features shape and size. These features are then serving as an etchmask in a fluorine plasma. The organic etch resist is then removed either in an oxygen plasma or in a piranha solution. AFM analysis revealed that 3 to 4 nm wide defined structures were obtained using C96 as the etch mask. This is about ten times smaller then industry standards. Also a depth profile of 50 nm, which is the minimum feature depth used in industry, was created using a fullerene containing polymer as the etch mask. Directionality and control over the shape and sizes of the features are naturally critical for implementing this technology in device fabrication. Therefore, alignment of the materials used has also been examined. Monolayers of highly stable molecules has successfully been used as etch masks. Further research and development could implement molecular lithography in device fabrication. Self-assembly among other forces would dictate which materials could be used successfully as a molecular resist.

Self-assembled monolayers have been proven to be well-ordered and to give stable ultrathin films. They show a remarkably high diversity with respect to their functionalisation giving rise to many possible applications. This thesis is focused on the potential use of these molecular thin films in life sciences. The reproduction of a membrane-like environment with these tightly packed and organized unimolecular layers has led to important breakthroughs in their nanotechnological application as biomaterials. Their straightforward modification allows the chemical and physical properties of biological interfaces to be altered. In particular, Oligo(ethylene glycol) based alkanethiol self-assembled monolayers were intensively studied as biointerfaces for their ability to resist the non specific adsorption of proteins. The electrostatic repulsion which originates from these monolayers was seen as one of the possible factors causing this protein repulsion. On the other hand proteins adsorb on alkanethiol self-assembled monolayers. This can be partially attributed to an attractive hydrophobic interaction between the biomolecules and the surface. As a result of the understanding of these two driving forces which are relevant for non-specific protein adsorption/repulsion, novel self-assembling molecules were tailored in an attempt to adjust the adsorption of proteins at the SAM-liquid interface. This was conceivable with these newly designed SAMs since they allow a combination of these forces. We have chosen the ionic strength of the liquid environment as the external parameter which could act on the amount of adsorbed proteins because the electrostatic force created by oligo(ethylene glycol) groups depends on it. In addition to the synthesis of six new molecules, the preparation and characterisation of the novel self-assembled monolayers are reported in this thesis. The density of the monolayers was estimated by X-ray photoelectron spectroscopy and ellipsometry, and the wettability properties were studied by measuring the contact angle. The total force acting on proteins from the SAMs was studied with an atomic force microscope, equipped with a tip mimicking proteins, by measuring force-distance curves. An in-situ technique was investigated in order to study the influence of the variation of this total force on the quantity of adsorbed proteins by varying the ionic strength.

The contamination of drinking water by microbial pathogens is recognized as one of the most pressing water supply problems of our day. To minimize the impact of pathogens and parasites on the environment and public health, accurate methods are needed to evaluate their presence and concentration. Although various techniques exist to detect certain pathogens in water (e.g., immunofluorescence or PCR techniques), these are time- and labor-intensive. A direct, real-time method for detection and quantification of target organisms would thus be very useful for rapid diagnosis of water safety. A quartz crystal microbalance with dissipation monitoring (QCM-D) based biosensor for detection of waterborne pathogens (i.e., Escherichia coli O157:H7) was developed. The detection platform is based on the immobilization of affinity purified antibodies onto gold coated QCM-D quartz crystals via a cysteamine self-assembled monolayer. The results show that the optimal sensor response is the initial slope of the dissipation shift. A highly log-log linear response is obtained for detection of E. coli O157:H7 over a broad range of cell concentration from 3 x 105 to 1 x 109 cells/mL. The prepared biosensor also exhibits a log-log linear working range from 107 to 109 cells/mL for E. coli K12 D21, a non-pathogenic model organism. The biosensor also shows satisfactory selectivity using Bacillus subtilis . To our knowledge, this is the first study demonstrating the use of the slope of the dissipation shift as a sensor response when using QCM-D technology. / Keywords: Biosensor, QCM-D, E. coli O157:H7, polyc1onal antibodies, dissipation slope, cysteamine, self-assembled monolayer