Nanofabrication techniques were used to manufacture nanometer scale protein templates. The fabrication approach employs electron beam lithography (EBL) patterning on poly(ethylene glycol) (PEG) thiol (CH3O(CH2CH2O)17NHCO(CH2)2SH) self-assembled monolayers (SAM) on Au. The PEG SAM prevented protein surface adhesion and binding sites for protein were created in the SAM by EBL. Subsequent to EBL, the patterns in the PEG SAM were backfilled with 40-nm NeutrAvidin-coated fluorescent spheres (FluoSpheres). The spontaneous and directed immobilization of the spheres from a solution to the patterns resulted in high resolution protein patterns. The FluoSpheres could be arranged in any arbitrary pattern with ultimately only one or a few FluoSpheres at each binding site. Growth dynamics and SAM morphology of PEG on Au were studied by atomic force microscopy (AFM). PEG SAMs on three types of Au with different microstructure were examined: thermally evaporated granular Au and two types of Au films produced by hydrogen flame annealing of granular Au, Au(111) and "terraced" Au (crystal orientation unknown). The different Au surfaces' substructure affected the morphology and mechanical properties of the PEG SAM. On Au(111), AFM imaging revealed monolayer formation through three distinct steps: island nucleation, island growth, and coalescence. The fine-structure of the SAM revealed dendritic island formation - an observation which can be explained by attractive intermolecular interactions and diffusion-limited aggregation. Island growth was not observed on the "terraced" Au. AFM studies of EBL patterned PEG SAMs on Au(111) revealed two different patterning mechanisms. At low doses, the pattern formation occurs by SAM ablation in a self-developing process where the feature depth is directly dose dependent. At higher doses electron beam induced deposition of material, so-called contamination writing, is seen in the ablated areas of the SAM. The balance between these two mechanisms is shown to depend on the geometry of the pattern. In addition to PEG SAMs, fibronectin monolayers on SiO2 surfaces were patterned by EBL. The areas exposed with EBL lose their functionality and do not bind anti-fibronectin. With this approach we constructed fibronectin templates and used them for cell studies demonstrating pattern dependent cell geometries and cell adhesion. / QC 20101008

A novel cyclopentadienylruthenium(II) thiolato Schiff base, [Ru(SC6H4NC(H)C6H4OCH2CH2SMe)(&eta / 5-C2H5]2 was synthesized and deposited as a selfassembled monolayer (SAM) on a gold electrode. Effective electronic communication between the Ru(II) centers and the gold electrode was established by electrostatically cycling the Shiff base-doped gold electrode in 0.1 M NaOH from -200 mV to +600 mV. The SAMmodified gold electrode (Au/SAM) exhibited quasi-reversible electrochemistry. The integrity of this electro-catalytic SAM, with respect to its ability to block and electro-catalyze certain Faradaic processes, was interrogated using Cyclic and Osteryoung Square Wave voltammetric experiments. The formal potential, E0', varied with pH to give a slope of about - 34 mV pH-1. The surface concentration, &Gamma / , of the ruthenium redox centers was found to be 1.591 x 10-11 mol cm-2. By electrostatically doping the Au/SAM/Horseradish peroxidase at an applied potential of +700 mV vs Ag/AgCl, a biosensor was produced for the amperometric analysis of hydrogen peroxide, cumene hydroperoxide and tert-butylhydroperoxide. The electrocatalytic-type biosensors displayed typical Michaelis-Menten kinetics with their limits of detection of 6.45 &mu / M, 6.92 &mu / M and 7.01 &mu / M for hydrogen peroxide, cumene hydroperoxide and tert-butylhydroperoxide respectively.

The work described in this thesis aims to achieving surface patterning through chemical activation of thiolated silicon oxide surfaces, resulting in a spatially controlled covalent immobilization of biomolecules with high resolution. Existing chemical methods to immobilize molecules on surfaces do not reach below the micrometer scale while the ones allowing for spatial control mostly lead to non-covalent adsorption of molecules on surfaces, or require several successive chemical reactions to obtain the final covalent immobilization. Methods with improved chemical processes and novel surface modification techniques had to be developed. A basic need for studying interactions of biomolecules on chemically modified surfaces with high resolution is the ability to obtain a simple, inexpensive method resulting in ultraflat densely packed and reproducible organic monolayers. Therefore, a new method for silicon oxide chemical derivatization, fulfilling these requirements, was developed. Thiol derivatized silicon oxide surfaces allow for a diversity of activation reactions to occur, resulting in thiol-disulfide exchange. The electrooxidation of surface-bound thiol groups was investigated as a way of generating reactive thiolsulfinates/thiolsulfonates, by application of a positive potential difference to the silicon surfaces. Peptide molecules containing thiol groups were successfully immobilized to the electroactivated surfaces. In addition, this new chemical activation method offers the possibility to release the bound molecules in order to regenerate the surfaces. Subsequently, the thiolated surfaces can be reactivated for further use. Since the activated area depends directly on the size of the electrodes used for the oxidation, nanoscale activation of the thiolated surfaces was performed by use of an AFM tip as counter-electrode. Electrooxidized patterns, with a line width ranging from 70 nm to 200 nm, were obtained. A thiol-rich protein, b-galactosidase, was selectively immobilized onto the electroactivated patterns. An electrochemical version of microcontact printing was developed in order to activate large surface areas with micrometer scale patterns. Conductive soft polymer stamps were produced using an evaporated aluminum coating. Patterned electroactivation of thiols was achieved, and polystyrene beads were subsequently specifically immobilized onto the patterns. As a conclusion, these different projects resulted in a strategy enabling the achievement of nanoscale and microscale positioning and immobilization of biomolecules on silicon surfaces, with potential reversibility and reuse of the surfaces.

The study and understanding of molecular interactions is fundamentally important in today's field of life sciences and there is a demand for well designed surfaces for biosensor applications. The biosensor has to be able to detect specific molecular interactions, while non-specific binding of other substances to the sensor surface should be kept to a minimum.                                                                                                                                                                                The objective of this master´s thesis was to design sensor surfaces based on self-assembled monolayers (SAMs) and evaluate their structural characteristics as well as their performance in Biacore systems. By mixing different oligo (ethylene glycol) terminated thiol compounds in the SAMs, the density of functional groups for bimolecular attachment could be controlled.  Structural characteristics of the SAMs were studied using Ellipsometry, Contact Angle Goniometry, IRAS and XPS. Surfaces showing promising results were examined further with Surface Plasmon Resonance in Biacore instruments.Mixed SAM surfaces with a tailored degree of functional COOH groups could be prepared. The surfaces showed promising characteristics in terms of stability, immobilization capacity of biomolecules, non-specific binding and kinetic assay performance, while further work needs to be dedicated to the improvement of their storage stability. In conclusion, the SAM based sensor surfaces studied in this thesis are interesting candidates for Biacore applications.

This thesis details the development of expertise and tools required for the study of amino acids deposited on Au(111), with a primary focus on the design and testing of a Knudsen cell for controlled deposition of L-cysteine and L-methionine. An ultra-high vacuum preparation chamber designed by Dr. Katie Mitchell and built by Torrovap Industries Inc. was installed. This chamber is connected to the existing scanning tunneling microscopy chamber via a gate valve, and both chambers can operate independently. Various instruments such as a mass spectrometer, quartz crystal microbalance, ion source, and sample manipulator were installed on the preparation chamber. Scanning tunneling microscopy was performed on both homemade and commercial Au(111) thin films. High resolution images of "herringbone" reconstruction and individual atoms were obtained on the commercial thin films, and optimal tunneling conditions were determined. A Knudsen cell was designed to be mounted on the preparation chamber. The Knudsen cell operates over the temperature range 300-400K, with temperatures reproducible to ±0.5K, and stable to ±0.1K over a five minute period. Reproducible deposition rates of less than 0.2Ǻ/s were obtained for both L-cysteine and L-methionine. Electron impact mass spectrometry and heat of sublimation measurements were performed to characterize the effusion of L-cysteine and L-methionine from the Knudsen cell. The mass spectrometry results suggest that L-cysteine was decomposing at 403K while L-methionine was stable during effusion. Heats of sublimation of 168.3±33.2kJ/mol and 156.5±10.1kJ/mol were obtained for L-cysteine and L-methionine respectively.

One the most daunting technical challenges in the realization of biosensors is functionalizing transducing surfaces for the detection of biomolecules. Functionalization is defined as the formation of a bio-compatible interface on the transducing surfaces of bio-chemical sensors for immobilizing and subsequent sensing of biomolecules. The kinetics of functionalization reactions is a particularly important issue, since conventional functionalization protocols are associated with lengthy process times, from hours to days. The objective of this thesis is the improvement of the functionalization protocols and their kinetics for biosensing applications. This objective is realized via modeling and experimental verification of novel functionalization techniques in microfluidic environments. The improved functionalization protocols using microfluidic environments enable in-situ functionalization, which reduces the processing times and the amount of reagents consumed, compared to conventional methods. The functionalization is performed using self-assembled monolayers (SAMs) of thiols. The thiols are organic compounds with a sulphur group that assists in the chemisorption of the thiol to the surface of metals like gold. The two reactions in the functionalization process examined in this thesis are the SAM formation and the SAM/probe molecule conjugation. SAM/probe molecule conjugation is the chemical treatment of the SAM followed by the binding of the probe molecule to the SAM. In general, the probe molecule is selective in binding with a given biomolecule, called the target molecule. Within this thesis, the probe molecule is an antibody and the target molecule is an antigen. The kinetics of the reaction between the probe (antibody) and the target biomolecule (antigen) is also studied. The reaction between an antigen and its antibody is called the immunoreaction. The biosensing technique that utilizes the immunoreaction is immunoassay. A numerical model is constructed using the finite element method (FEM), and is used to study the kinetics of the functionalization reactions. The aim of the kinetic studies is to achieve both minimal process times and reagents consumption. The impact of several important parameters on the kinetics of the reactions is investigated, and the trends observed are explained using kinetic descriptive dimensionless numbers, such as the Damköhler number and the Peclet number. Careful numerical modeling of the reactions contributes to a number of findings. A considerably faster than conventional SAM formation protocol is predicted. This fast-SAM protocol is capable of reducing the process times from the conventional 24-hours to 15 minutes. The numerical simulations also predict that conventional conjugation protocols result in the overexposure of the SAM and the probe molecule to the conjugation reagents. This overexposure consequently lowers conjugation efficiencies. The immunoreaction kinetics of a 70 kilo-Dalton heat shock protein (HSP70) with its antibody in a hypothetical microchannel is also investigated through the FEM simulations. Optimal reaction conditions are determined, including the flow velocity and the surface concentration of the immobilized probes (antibodies). Based on the numerical results and a series of experimental studies, the fast-SAM protocol application is successfully confirmed. Moreover, the optimum reagent concentration for a given one- hour conjugation process time is determined. This functionalization protocol is successfully applied to immobilize the HSP70 antibody on gold surfaces. The use of the fast-SAM protocol and the predicted optimum conjugation conditions result in binding of the HSP70 antibody on gold, with the same or superior immobilization quality, compared to the conventional protocols. Upon implementation of a 70 μm.s^(-1) flow velocity, the reaction is observed to complete in around 30-35 minutes, which is close to the numerically predicted 30 minutes and 16 seconds. This immunoreaction time is considerably less than conventional 4-12 hour processes. The modified in-situ functionalization techniques achieved here are promising for substantially reducing the preparation times and improving the performance of biosensors, in general, and immunoassays, in particular.

This thesis details the development of expertise and tools required for the study of amino acids deposited on Au(111), with a primary focus on the design and testing of a Knudsen cell for controlled deposition of L-cysteine and L-methionine. An ultra-high vacuum preparation chamber designed by Dr. Katie Mitchell and built by Torrovap Industries Inc. was installed. This chamber is connected to the existing scanning tunneling microscopy chamber via a gate valve, and both chambers can operate independently. Various instruments such as a mass spectrometer, quartz crystal microbalance, ion source, and sample manipulator were installed on the preparation chamber. Scanning tunneling microscopy was performed on both homemade and commercial Au(111) thin films. High resolution images of "herringbone" reconstruction and individual atoms were obtained on the commercial thin films, and optimal tunneling conditions were determined. A Knudsen cell was designed to be mounted on the preparation chamber. The Knudsen cell operates over the temperature range 300-400K, with temperatures reproducible to ±0.5K, and stable to ±0.1K over a five minute period. Reproducible deposition rates of less than 0.2Ǻ/s were obtained for both L-cysteine and L-methionine. Electron impact mass spectrometry and heat of sublimation measurements were performed to characterize the effusion of L-cysteine and L-methionine from the Knudsen cell. The mass spectrometry results suggest that L-cysteine was decomposing at 403K while L-methionine was stable during effusion. Heats of sublimation of 168.3±33.2kJ/mol and 156.5±10.1kJ/mol were obtained for L-cysteine and L-methionine respectively.

<p>Nanofabrication techniques were used to manufacture nanometer scale protein templates. The fabrication approach employs electron beam lithography (EBL) patterning on poly(ethylene glycol) (PEG) thiol (CH3O(CH2CH2O)17NHCO(CH2)2SH) self-assembled monolayers (SAM) on Au. The PEG SAM prevented protein surface adhesion and binding sites for protein were created in the SAM by EBL. Subsequent to EBL, the patterns in the PEG SAM were backfilled with 40-nm NeutrAvidin-coated fluorescent spheres (FluoSpheres). The spontaneous and directed immobilization of the spheres from a solution to the patterns resulted in high resolution protein patterns. The FluoSpheres could be arranged in any arbitrary pattern with ultimately only one or a few FluoSpheres at each binding site.</p><p>Growth dynamics and SAM morphology of PEG on Au were studied by atomic force microscopy (AFM). PEG SAMs on three types of Au with different microstructure were examined: thermally evaporated granular Au and two types of Au films produced by hydrogen flame annealing of granular Au, Au(111) and "terraced" Au (crystal orientation unknown). The different Au surfaces' substructure affected the morphology and mechanical properties of the PEG SAM. On Au(111), AFM imaging revealed monolayer formation through three distinct steps: island nucleation, island growth, and coalescence. The fine-structure of the SAM revealed dendritic island formation - an observation which can be explained by attractive intermolecular interactions and diffusion-limited aggregation. Island growth was not observed on the "terraced" Au.</p><p>AFM studies of EBL patterned PEG SAMs on Au(111) revealed two different patterning mechanisms. At low doses, the pattern formation occurs by SAM ablation in a self-developing process where the feature depth is directly dose dependent. At higher doses electron beam induced deposition of material, so-called contamination writing, is seen in the ablated areas of the SAM. The balance between these two mechanisms is shown to depend on the geometry of the pattern.</p><p>In addition to PEG SAMs, fibronectin monolayers on SiO2 surfaces were patterned by EBL. The areas exposed with EBL lose their functionality and do not bind anti-fibronectin. With this approach we constructed fibronectin templates and used them for cell studies demonstrating pattern dependent cell geometries and cell adhesion.</p>

Τα αυτό -οργανούμενα μονοστρωματικά συστήματα (self-assembled monolayers, SAMs) παρουσιάζουν μεγάλο τεχνολογικό και βιομηχανικό ενδιαφέρον καθώς προσφέρουν μοναδική ευκαιρία για την κατανόηση των διεπιφανειακών φαινομένων και των διεργασιών που σχετίζονται με αυτά. Ο έλεγχος των ιδιοτήτων διαβροχής και λίπανσης της επιφάνειας , η επιλεκτική ρόφηση διαφόρων ειδών μορίων (π .χ ., μεγάλων βιολογικών μορίων) για το σχηματισμό επιπρόσθετου μονοστρώματος προς μία προεπιλεγμένη δομή (π.χ ., με συγκεκριμένο μοριακό προσανατολισμό), ο σχεδιασμός βιοαισθητήρων αλλά και άλλα παραδείγματα αποτελούν μερικές μόνο από τις πιο διαδεδομένες εφαρμογές των SAMs. Στην παρούσα εργασία εστιάσαμε στο πιο διαδεδομένο σύστημα SAM, αυτό που δημιουργείται κατά τη ρόφηση μορίων αλκανοθειολών σε επιφάνεια χρυσού (R-SH/ Au(111)). Πιο συγκεκριμένα διερευνήσαμε τις δομικές ιδιότητες καθώς και τις ιδιότητες διαμόρφωσης του σχηματιζόμενου μονοστρώματος με τη βοήθεια ενός καινούργιου αλγορίθμου Monte Carlo (MC) που σχεδιάσαμε στο εργαστήριο, βασισμένου σ’ ένα ιδιαίτερα αποδοτικό μίγμα τόσο απλών όσο και πιο σύνθετων (συχνά μη φυσικών) κινήσεων για τη δειγματοληψία απεικονίσεων του συστήματος. Η καινοτομία του αλγόριθμου MC συνίσταται στο ότι, ανεξάρτητα από την αρχική απεικόνιση του συστήματος, έχει την ικανότητα να οδηγεί αποτελεσματικά όλα τα μόρια της αλκανοθειόλης επάνω στο υπόστρωμα του χρυσού με αποτέλεσμα στο τέλος της προσομοίωσης αυτό να χαρακτηρίζεται από 100% επιφανειακή κάλυψη. Κατά τον τρόπο αυτό παρακάμπτεται ένας σημαντικός περιορισμός των προηγούμενων μεθόδων , οι οποίες ουσιαστικά προ-υπέθεταν την αρχική απεικόνιση του συστήματος (στη βάση πειραματικών δεδομένων). Επιπλέον, λαμβάνοντας υπόψη ένα εκτεταμένο σύνολο αντιγράφων του συστήματος καθένα από τα οποία προσομοιώνεται σε μία διαφορετική τιμή της διαμέτρου van der Waals των ατόμων θείου, σss, και επιχειρώντας ανταλλαγές απεικονίσεων μεταξύ συστημάτων με παρακείμενες τιμές σss, ο νέος αλγόριθμος μας επέτρεψε να προσομοιώσουμε αποτελεσματικά πρότυπα συστήματα R-SH/Au(111) για ένα φάσμα τιμών της παραμέτρου σss από 4.25 Å που αντιστοιχεί στο μοριακό μοντέλο των Hautman-Klein [J. Chem. Phys., 1988; 1989] έως 4.97 Å που αντιστοιχεί στο μοριακό μοντέλο των Siepmann-McDonald [Langmuir, 1993]. Η εφαρμογή του αλγορίθμου MC επεκτάθηκε ακολούθως σε συστήματα αλκανοθειολών ροφημένων σε διαφορετικά μεταλλικά υποστρώματα, με σκοπό τη μελέτη της επίδρασης του είδους της μεταλλικής επιφάνειας στις δομικές ιδιότητες των συστημάτων SAMs. Προς την κατεύθυνση αυτή, αρχικά εκτελέστηκαν κβαντομηχανικοί υπολογισμοί ( ab initio calculations) για ένα μόριο μεθανοθειόλης ροφημένου σε επιφάνεια χρυσού, αργύρου ή πλατίνας και τα αποτελέσματα χρησιμοποιήθηκαν για την εξαγωγή ενός κλασσικού δυναμικού για την περιγραφή των αλληλεπιδράσεων μεταξύ θείου -μετάλλου. Με το δυναμικό αυτό διεξήχθησαν στη συνέχεια ατομιστικές προσομοιώσεις MC για διάφορα μοριακά μήκη συστημάτων SAMs R-SH και στη συνέχεια έγινε ανάλυση των δεδομένων, με έμφαση στην εξάρτηση των δομικών ιδιοτήτων του σχηματιζόμενου φιλμ (μοριακός προσανατολισμός, διαμόρφωση αλυσίδων και στατιστική των ατελειών gauche) από τη φύση του μεταλλικού υποστρώματος. Στο τελευταίο στάδιο της διατριβής εστιάσαμε στη μελέτη της θερμοκρασίας υαλώδους μετάπτωσης Tg ισότροπων συστημάτων αλλά και λεπτών υμενίων πολυαιθυλενίου (PE) με τις αλυσίδες εμφυτευμένες σε σκληρή, ενθαλπικά ουδέτερη επιφάνεια και σχετικά μεγάλη πυκνότητα εμφύτευσης. Για το λόγο αυτό επεκτάθηκε η μεθοδολογία προσομοίωσης MC σε χαμηλές θερμοκρασίες (κοντά στο ή ακόμα και χαμηλότερα από το σημείο Tg) χρησιμοποιώντας την πολύ δραστική κίνηση MC αναγεφύρωσης άκρων (end-bridging, EB). Τα δεδομένα της προσομοίωσης για την εξάρτηση της πυκνότητας και της ενθαλπίας από την θερμοκρασία χρησιμοποιήθηκαν για τον υπολογισμό της θερμοκρασίας υαλώδους μετάπτωσης, με το αποτέλεσμα να συμφωνεί σχεδόν επακριβώς με την αντίστοιχη πειραματική τιμή για ημικρυσταλλικό πολυαιθυλένιο στο όριο μηδενικού βαθμού κρυσταλλικότητας (προβλεπόμενη τιμή Tg μεταξύ 220 και 240 Κ). / Self-assembled monolayers (SAMs) find numerous applications in a variety of fields: in the production of thin films from organic materials, in optics and electronics, as means for controlling the hydrophobic or hydrophilic behavior of a surface, as coatings for the protection of surfaces from corrosion, in molecular recognition, and more recently even as biosensors. In an effort to understand the mechanisms and interactions controlling chain organization and packing in these systems and how these affect their macroscopic properties, the present thesis has focused on the development of a Monte Carlo (MC) algorithm, built around a set of simpler but also more complex (sometimes non-physical) moves, for the atomistic simulation of the SAM structures formed by the adsorption of short alkanethiol molecules on a Au(111) surface. The innovation of the MC algorithm is that it is capable of efficiently driving all alkanethiol molecules to the Au(111), thereby leading to full surface coverage, irrespective of the initial setup of the system. This circumvents a significant limitation of previous methods in which the simulation typically starts from optimally packed structures on the substrate that are close to thermal equilibrium. Further, by considering an extended ensemble of configurations each one of which corresponds to a different value of the sulphur-sulphur repulsive core potential, σ ss , and by allowing for configurations to swap between different σ ss values, the new algorithm can adequately simulate model R-SH/ Au(111) systems for values of σ ss ranging from 4.25 Å corresponding to the Hautman-Klein molecular model [J. Chem. Phys., 1988; 1989] to 4.97 Å corresponding to the Siepmann-McDonald model [Langmuir, 1993]. A thorough investigation of the variation of molecular organization and ordering on the Au(111)substrate with chain length is presented. In a parallel study, the MC method was extended to alkanethiol SAM systems on different metal surfaces. This has allowed us to perform a detailed investigation of the substrate’s effect on the structure and conformation of the above systems through atomistic MC simulations based on a first-principles density functional modeling of the sulphur-metal interaction. Ab initio calculations on a methanethiol molecule adsorbed on gold, silver and platinum surfaces were conducted and the data obtained were used to develop an accurate classical force field which served as an input to the new MC algorithm. Emphasis was given primarily to the study of the effect of the substrate on the structural properties of the simulated R-SH SAM systems, like molecular orientation, molecular conformation, and statistics of gauche defects. In the last part of this thesis, and in an attempt to investigate the phenomenon of glass transition ( Tg ), the MC algorithm was employed in simulations with a less complex, than the SAM structures, system, that of amorphous polyethylene (PE). Two sets of simulations were executed: one with a bulk, isotropic sample, and the other with a thin film in which all PE chains were grafted on a hard surface on the one side and exposed to vacuum on the other. In all cases, the simulations were carried out for very long times in order for the autocorrelation function of the chain end-to-end vector to drop practically to zero. For both systems, the value of the glass transition temperature Tg was extracted using volumetric and enhtalpic simulation data and it was found to be between 220 and 240K, i.e., in remarkable agreement with measured data for semicrystalline PE in the limit of zero crystallinity. Additional results about the temperature dependence of the conformational (e.g., the equilibrium mean-square chain end-to-end distance) and structural (e.g., the intermolecular pair distribution function) properties in the two PE systems were also obtained and discussed in detail.

Graphene, a two-dimensional counterpart of three-dimensional graphite, has attracted significant interest, due to its distinctive electrical and mechanical properties, for developing electronic, optoelectronic, and sensor technologies. In general, doping of graphene is important, as it gives rise to p-type and n-type materials, and it adjusts the work function of the graphene. This adjustment is necessary in order to control charge injection and collection in devices such as solar cells and light emitting devices. Current methods for graphene doping involve high temperature process or interactions with chemicals that are not stable. Moreover, the process of transferring graphene from its growth substrate and its exposure to the environment results in a host of chemical groups that can become attached to the film and alter its electronic properties by accepting or donating electrons/holes. Intentional and controllable doping of the graphene, however, requires a deeper understanding of the impact of these groups. The proposed research will attempt to clarify the unintentional doping mechanism in graphene through adsorption or desorption of gas/vapor molecules found in standard environments. A low temperature, controllable and defect-free method for doping graphene layers will also be studied through modifying the interface of graphene and its support substrate with self-assembled monolayers (SAMs) which changes the work function and charge carriers in the graphene layer. Furthermore, current methods of chemical vapor deposition synthesis of graphene requires the film to be transferred onto a second substrate when the metal layer used for growth is not compatible with device fabrication or operation. To address this issue, the proposed work will investigate a new method for wafer scale, transfer-free synthesis of graphene on dielectric substrates using new carbon sources. This technique allows patterned synthesis on the target substrate and is compatible with standard device fabrication technologies; hence, it opens a new pathway for low cost, large area synthesis of graphene films.