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Yes / Investigation of the non-covalent interaction of biomolecules with aqueous graphene interfaces is a rapidly expanding area. However, reliable exploitation of these interfaces in many applications requires that the links between the sequence and binding of the adsorbed peptide structures be clearly established. Molecular dynamics (MD) simulations can play a key role in elucidating the conformational ensemble of peptides adsorbed at graphene interfaces, helping to elucidate these rules in partnership with experimental characterisation. We apply our recently-developed polarisable force-field for biomolecule–graphene interfaces, GRAPPA, in partnership with advanced simulation approaches, to probe the adsorption behaviour of peptides at aqueous graphene. First we determine the free energy of adsorption of all twenty naturally occurring amino acids (AAs) via metadynamics simulations, providing a benchmark for interpreting peptide–graphene adsorption studies. From these free energies, we find that strong-binding amino acids have flat and/or compact side chain groups, and we relate this behaviour to the interfacial solvent structuring. Second, we apply replica exchange with solute tempering simulations to efficiently and widely sample the conformational ensemble of two experimentally-characterised peptide sequences, P1 and its alanine mutant P1A3, in solution and adsorbed on graphene. For P1 we find a significant minority of the conformational ensemble possesses a helical structure, both in solution and when adsorbed, while P1A3 features mostly extended, random-coil conformations. In solution this helical P1 configuration is stabilised through favourable intra-peptide interactions, while the adsorbed structure is stabilised via interaction of four strongly-binding residues, identified from our metadynamics simulations, with the aqueous graphene interface. Our findings rationalise the performance of the P1 sequence as a known graphene binder. / veski

I measured the transport properties of graphene nanoribbons as a function of the charged impurity density in ultra-high vacuum to directly probe the effect of dimensional confinement. Coulomb impurities create charge puddles in graphene sheets, which dominate transport properties. My results shed light on recent predictions about the fundamental mechanisms behind gaps in conductance that appear in transport measurements.

Résumé : Nous étudions dans cette thèse plusieurs propriétés du gaz d’électrons bidimensionnel (GE2D) dans le graphène et la bicouche de graphène (BG). Nous commençons par étudier la nature des excitations à une particule du GE2D dans le graphène près des facteurs de remplissage entiers dans les niveaux de Landau N [pas égal à] 0. Nous utilisons une approche de type Hartree-Fock (HF) pour comparer l’énergie de l’excitation d’une paire électron-trou à celle d’une paire skyrmion (SK)-antiskyrmion (ASK). Dans le graphène, les excitations SK et ASK sont des excitations chargées avec une texture de spin et/ou de pseudospin de vallée qui est quantifiée topologiquement. Nos calculs montrent que les paires SK-ASK sont les excitations chargées de plus basse énergie jusqu’au niveau de Landau |N| = 3. Notre approche permet en plus de calculer le domaine de couplage Zeeman pour lequel les paires SK-ASK sont les excitations de plus basse énergie et de déterminer comment l’énergie de ces paires est modifiée par les corrections d’écrantage. Le diagramme de phase du GE2D dans la bicouche de graphène a fait l’objet d’intenses recherches théoriques et expérimentales [8, 13, 15, 16], mais jusqu’à maintenant, seuls les états uniformes ont été considérés. Nous adaptons notre approche HF à l’étude des états non uniformes pour montrer que le GE2D dans la BG à remplissage ν = −1 dans le niveau de Landau N = 0 subit une série de transitions de phase lorsqu’un champ électrique perpendiculaire à la BG est appliqué. Nous étudions tout particulièrement les phases comportant une texture de pseudospin orbital soit un cristal de skyrmions et une phase spirale. Nous calculons les modes collectifs de ces phases ainsi que leur absorption électromagnétique. Nous poursuivons ensuite avec une étude des phases cristallines autour de certains remplissages entiers dans la BG. Le GE2D dans la bicouche de graphène a principalement été étudié dans le niveau de Landau N = 0. Comme dernier problème, nous étudions le diagramme de phase lorsqu’un nombre entier de niveaux de Landau est occupé dans les niveaux supérieurs |N| > 0. Alors que l’état fondamental du GE2D dans le graphène pour ces mêmes niveaux est un ferroaimant de Hall quantique (FHQ) avec une symétrie SU(2) pour le spin (en l’absence de couplage Zeeman) et le pseudospin de vallée, le GE2D dans la BG a plutôt un comportement FHQ de type Ising avec une symétrie Z[indice inférieur 2] à champ électrique nul. Cette différence de comportement a une grande influence sur la nature des transitions de phase possibles ainsi que sur celle des excitations topologiques. // Abstract : In this thesis, we study several properties of the two-dimensional electron gas (2DEG) in graphene and bilayer graphene. We first study the nature of the single-particle excitations in graphene near integer filling factors in Landau levels (LLs) N [not equal to] 0. We use a Hartree-Fock approach to compare the energy of an electron-hole excitation pair with that of a Skyrmion-antiskyrmion pair. In graphene, Skyrmions are charged excitations with a topological quantized spin and/or valley pseudo-spin texture. We give the range of Zeeman coupling for which Skyrmion-antiskyrmion has the lowest energy up to LL N = 3. Then we discuss how screening corrections modifies these results. The phase diagram of the 2DEG in bilayer graphene had been studied previously by a number of authors [8, 13, 15, 16] but only uniform states had been considered. Extending the Hartree-Fock approach to non-uniform states, we show that at filling factor ν = −1 in LL N = 0, the 2DEG goes through a series of phase transitions as the bias from an external electric field between two layers is increased. We study a crystal phase with orbital SK textures and a spiral state with the orbital pseudospin rotating in space. We compute the collective mode of these phases and their signatures in electromagnetic absorption experiments. We finally extend the Hartree-Fock approach to study the crystal states with valley or orbital textures near integer filling factors. The research on the 2DEG in bilayer graphene has been focussed almost exclusively in LL N = 0. As our last problem, we study the phase diagram at quarter and half fillings of the quartet of states in LLs |N| > 0. While the ground state of the 2DEG in graphene in |N| > 0 is a valley and spin quantum Hall ferromagnet with SU(2) symmetry in the absence of Zeeman coupling, the ground state in bilayer graphene is an Ising quantum Hall ferromagnet with a Z[subscript 2] valley symmetry at zero bias. We note that this change has important consequences on the nature of the transport properties and the single-particle excitations at integer fillings.

First-principles calculations have been carried out to investigate structural and electronic properties of graphene on SiC and diamond substrates and for a study of doping of fluorographene with various surface adsorbates. New insight is given into the problem of the decoupling of the graphene layers from SiC substrates after epitaxial growth. Mechanisms of hydrogen penetration between graphene and SiC(0001) surface, and properties of hydrogen and fluorine intercalated structures have been studied. Energy barriers for diffusion of atomic and molecular hydrogen through the interface graphene layer with no defects and graphene layers containing Stone-Wales defect or two- and four-vacancy clusters have been calculated. It is argued that diffusion of hydrogen towards the SiC surface occurs through the hollow defects in the interface graphene layer. It is further shown that hydrogen easily migrates between the graphene layer and the SiC substrate and passivates the surface Si bonds, thus causing the graphene layer decoupling. According to the band structure calculations the graphene layer decoupled from the SiC(0001) surface by hydrogen intercalation is undoped, while that obtained by the fluorine intercalation is p-type doped. Further, structure and the electronic properties of single and double layer graphene on H-, OH-, and F- passivated (111) diamond surface have been studied. It is shown that graphene only weakly interacts with the underlying substrates and the linear dispersion of graphene pi-bands is preserved. For graphene on the hydrogenated diamond surfaces the charge transfer results in n-type doping of graphene layers and the splitting of conduction and valence bands in bilayer graphene. For the F- and OH-terminated surfaces, charge transfer and doping of graphene do not occur. Finally, the possibility of doping fluorographene by surface adsorbates have been investigated. The structure and electronic properties of fluorographene with adsorbed K, Li, Au atoms, and F4-TCNQ molecule are described. It is shown that adsorption of K or Li atoms results in electron doping of fluorographene, while Au atoms and F4-TCNQ introduce deep levels inside the band gap. The calculated value of the fluorographene work function is extremely high, 7.3 eV, suggesting that p-type doping is difficult to achieve.

The major objective of the research described in this dissertation is the development of new laser vaporization methods for the synthesis of metal and semiconductor nanoparticles, graphene, B- and N-doped graphene, and metal and semiconductor nanoparticles supported on graphene. These methods include the Laser Vaporization Controlled Condensation (LVCC) approach, which has been used in this work for the synthesis of: (1) gold nanoparticles supported on ceria and zirconia nanoparticles for the low temperature oxidation of carbon monoxide, and (2) graphene, boron- and nitrogen-doped graphene, hydrogen-terminated graphene (HTG), metal nanoparticles supported on graphene, and graphene quantum dots. The gold nanoparticles supported on ceria prepared by the LVCC method exhibit high activity for CO oxidation with a 100% conversion of CO to CO2 at about 60 °C. The first application of the LVCC method for the synthesis of these graphene and graphene-based nanomaterials is reported in this dissertation. Complete characterizations of the graphene-based nanomaterials using a variety of techniques including spectroscopic, X-ray diffraction, mass spectrometric and microscopic methods such as Raman, FTIR, UV-Vis, PL, XRD, XPS, TOF-MS, and TEM. The application of B- and N-doped graphene as catalysts for the oxygen reduction reaction in fuel cell applications is reported. The application of Pd nanoparticles supported on graphene for the Suzuki carbon-carbon cross-coupling reaction is reported. A new method is described for the synthesis of graphene quantum dots based on the combination of the LVCC method with oxidation/reduction sequences in solution. The N-doped graphene quantum dots emit strong blue luminescence, which can be tuned to produce different emission colors that could be used in biomedical imagining and other optoelectronic applications. The second method used in the research described in this dissertation is based on the Laser Vaporization Solvent Capturing (LVSC) approach, which has been introduced and developed, for the first time, for the synthesis of solvent-capped semiconductor and metal oxide nanoparticles. The method has been demonstrated for the synthesis of V, Mo, and W oxide nanoparticles capped by different solvent molecules such as acetonitrile and methanol. The LVSC method has also been applied for the synthesis of Si nanocrystals capped by acetonitrile clusters. The acetonitrile-capped Si nanocrystals exhibit strong emissions, which depend on the excitation wavelength and indicate the presence of Si quantum dots with different sizes. The Si and the metal oxide nanoparticles prepared by the LVSC method have been incorporated into graphene in order to synthesize graphene nanosheets with tunable properties depending on graphene-nanoparticle interactions.

The Graphene term has become synonymous with layered carbon sheets having thicknesses ranging from the monolayer to stacks of about ten layers. For bulk volume production, graphite chemical exfoliation is the preferred solution. For this reason, much interest has congregated around different processes to oxidize and peel off graphite to obtain graphene oxide (GO) and its counterpart, reduced GO (rGO). The community at-large has quickly adopted those processes and has been intensively using the resulting (r)GO as active materials for a myriad of applications. Yet, partially given the absence of comparative studies in synthesis methodologies, a lack of understanding persists on how to best tailor these carbon materials for a given application. In this dissertation, the effect of using different chemical oxidation-reduction strategies for graphite, namely the impact on the structure and chemistry of GOs and rGOs is systematically discussed. Added to this, it is demonstrated that the drying step of the powdered materials cannot be neglected. Its influence is demonstrated in studies such as the optimization of capacitance of rGOs touted as electrochemical energy storage materials (Chapter 4). It is concluded that, in order to maximize the performance of GO and rGO materials for any particular application, there must be a judicious choice of their synthesis steps. Obvious as it may be for anyone working in Chemistry, this point has been surprisingly overlooked for too long by the vast majority of those working with these carbon materials.

We analyze experimental evidence of transport through evanescent waves in graphene, reconciling existing experimental data with theory. We propose novel experimental geometries that provide even more compelling evidence of evanescent waves. We investigate the shot noise generated by evanescent modes in graphene for several experimental setups. For two impurity-free graphene strips kept at the Dirac point by gate potentials, separated by a long highly doped region, we find that the Fano factor takes the universal value F=1/4. For a large superlattice consisting of many strips gated to the Dirac point, interspersed among doped regions, we find F=1/(8ln2). These results differ from the value F=1/3 predicted for a disordered metal, providing an unambiguous experimental signature of evanescent mode transport in graphene. For a graphene nano-ribbon transistor geometry, we explain that the experimentally observed anomalous voltage scale of the shot noise can arise from doping by the contacts to the electrical circuit. These observations provide strong evidence of evanescent mode transport in graphene.

Graphene grown epitaxially on silicon carbide provides a potential avenue toward industrial-scale graphene electronics. A predominant aspect of the multilayer graphene produced on the carbon-terminated (000 -1) face of SiC is the rotational stacking faults between graphene layers and their associated moire-pattern superlattice. We use scanning tunneling microscopy (STM) and spectroscopy (STS) in high magnetic fields to obtain detailed information about the "massless Dirac fermions" that carry charge in graphene. In agreement with prior investigations, we find that for small magnetic fields, the rotational stacking effectively decouples the electronic properties of the top graphene layer from those below. However, in maps of the wavefunction density at magnetic fields above 5 Tesla, we discover atomic-scale features that were not previously known or predicted. A phenomenological theory shows that this high-field symmetry-breaking is a consequence of small cyclotron-orbit wavefunctions, which are sensitive to the local layer stacking structures internal to the moire superlattice cell. The broken symmetry is sublattice degeneracy, predicated by atomic scale variations that derive from the sublattice polarization of graphene wavefunctions.

Graphene, a sheet of carbon atoms organized in a honeycomb lattice, is a two dimensional crystal. Even though the material has been known for a long time, only recently has it stimulated considerable interest across different research areas. Graphene is interesting not only as a platform to study fundamental physics in two dimensions, but it also has great potential for post-silicon microelectronics owing to its exceptional electronic properties. Of the several methods known to produce graphene, epitaxial growth of graphene by sublimation of silicon carbide is probably the most promising for practical applications. This thesis is a theoretical study of the growth kinetics of epitaxial graphene on SiC(0001). We propose a step-flow growth model using coarse-grained kinetic Monte Carlo (KMC) simulations and mean-field rate equations to study graphene growth on both vicinal and nano-faceted SiC surfaces. Our models are consistent with experimental observations and provide quantitative results which will allow experimenters to interpret the growth morphology and extract energy barriers from experiments. Recently, it has been shown that graphene grown epitaxially on metal surfaces may lead to potential applications such as large area transparent electrodes. To study deposition-type epitaxial growth, we investigate a new theoretical approach to this problem called the phase field method. Compared to other methods this method could be less computationally intensive, and easier to implement at large spatial scales for complicated epitaxial growth situations.