Graphene, one-atom-thick planar sheet of carbon atoms densely packed in a honeycomb crystal lattice, has grabbed appreciable attention due to its exceptional electronic, mechanical and optical properties. Chemical functionalization schemes are needed to integrate graphene with the different materials required for potential applications. Molecular self-assembly behavior on graphene is a key method to investigate the mechanism of interaction between molecules and graphene and the promising applications related to molecular devices. In this thesis, we report the molecular self-assembly behavior of phenyl-C61-butyric acid methyl ester (PCBM), C60, perylenetetracarboxylic dianhydride (PTCDA) and Gd3N@C80 on flat and rippled graphene 2D material by the experimental methods of scanning tunneling microscope (STM) and atomic force microscope (AFM) and by the theoretical method of density functional theory (DFT). We found that molecules form ordered structures on flat graphene, while they form disordered structure on rippled graphene. For example, PCBM forms bilayer and monolayer structures, C60 and Gd3N@C80 form hexagonal close packed (hcp) structure on flat graphene and PTCDA forms herringbone structure on flat graphene surface. Although C60 and Gd3N@C80 both form hcp structure, C60 forms a highly ordered hcp structure over large areas with little defects and Gd3N@C80 forms hcp structure only over small areas with many defects. These differences of structure that forms on flat graphene is mainly due to the molecule-molecule interactions and the shape of the molecules. We find that the spherical C60 molecules form a quasi-hexagonal close packed (hcp) structure, while the planar PTCDA molecules form a disordered herringbone structure. From DFT calculations, we found that molecules are more effected by the morphology of rippled graphene than the molecule-molecule interaction, while the molecule-molecule interaction plays a main role during the formation process on flat graphene. The results of this study clearly illustrate significant differences in C60 and PTCDA molecular packing on rippled graphene surfaces. / Doctor of Philosophy / As the first physical isolated two-dimensional (2D) material, graphene has attracted exceptional scientific attention. Due to its impressive properties including high carrier density, flexibility and transparency, graphene has numerous potential applications, such as solar cell, sensors and electronics. 2D molecular self-assembly is an area that focuses on organization and interaction between self-assembly behaviors of molecules on surface. Graphene is an excellent substrate for the study of molecular self-assembly behavior, and study of molecular study is very important for graphene due to potential applications of molecules on graphene. In this thesis, we present investigations of the molecular self-assembly of PCBM, C60, PTCDA and Gd3N@C80 on graphene substrate. First, we report the two types of bilayer PCBM configuration on HOPG with a step height of 1.68 nm and 1.23 nm, as well as two types of monolayer PCBM configuration with a step height of 0.7 nm and 0.88 nm, respectively. On graphene, PCBM forms one type of PCBM bilayer with a step height of 1.37 nm and one type of PCBM monolayer with a step height of 0.87 nm. By building and analyzing the models of PCBM bilayers and monolayers, we believe the main differences between two configurations of PCBM bilayer and monolayer is the tilt angle between PCBM and HOPG, which makes type I configuration the higher molecule density and binding energy. Secondly, we report the investigation of self-assembly behaviors of C60 and PTCDA on flat graphene and rippled graphene by experimental scanning tunneling microscope (STM) and theoretical density functional theory (DFT). On flat graphene, C60 forms hexagon close pack (hcp) structure, while PTCDA forms herringbone structure. On rippled graphene, C60 forms quasi-hcp structure while PTCDA forms disordered herringbone structure. By DFT calculation, we study the effect of graphene curvature on spherical C60 and planar PTCDA. Finally, we report a STM study of a monolayer of Gd3N@C80 on graphene substrate. Gd3N@C80 forms hcp structure in a small domain with a step height of 0.88 nm and lattice constant of 1.15 nm. According to our DFT calculation, for the optimal organization of Gd3N@C80 and graphene, the gap between Gd3N@C80 and graphene is 3.3 Å and the binding energy is 0.95 eV. Besides, the distance between Gd3N@C80 and Gd3N@C80 is 3.5 Å and the binding energy is 0.32 eV.

Molecules adsorbed on two-dimensional (2D) materials can show interesting physical and chemical properties. This thesis presents scanning probe microscopy (SPM) investigation of emerging 2D materials, molecular nanostructures on 2D substrates at the nanometer scale, and biophysical processes on the biological membrane. Two main techniques of nano-probing are used: scanning tunneling microscopy (STM) and atomic force microscopy (AFM). The study particularly emphasizes on self-assembled molecules on flat 2D materials and quasi-1D wrinkles. First, we report the preparation of novel 1D C60 nanostructures on rippled graphene. Through careful control of the subtle balance between the linear periodic potential of rippled graphene and the C60 surface mobility, we demonstrate that C60 molecules can be arranged into a 1D C60 chain structure of two to three molecules in width. At a higher annealing temperature, the 1D chain structure transitions to a more closely packed, quasi-1D hexagonal stripe structure. The experimental realization of 1D C60 structures on graphene is, to our knowledge, the first in the field. It could pave the way for fabricating new C60/graphene hybrid structures for future applications in electronics, spintronic and quantum information. Second, we report a study on nano-morphology of potential operative donors (e.g., C60) and acceptors (e.g., perylenetetracarboxylic dianhydride, aka. PTCDA) on wrinkled graphene supported by copper foils. We realize sub-monolayer C60 and PTCDA on quasi-1D and quasi-2D real periodic wrinkled graphene, by carefully controlling the deposition parameters of both molecules. Our successful realization of acceptor-donor binary nanostructures on wrinkled graphene could have important implications in future development of organic solar cells. Third, we report an STM and spectroscopy study on atomically thin transition-metal dichalcogenides (TMDCs) material. TMDCs are emerging 2D materials recently due to their intriguing physical properties and potential applications. In particular, our study focuses on molybdenum disulfide (MoS2) mono- to few-layers and pyramid nanostructures synthesized through chemical vapor deposition. On the few-layered MoS2 nanoplatelets grown on gallium nitride (GaN) and pyramid nanostructures on highly oriented pyrolytic graphite (HOPG), we observe an intriguing curved region near the edge terminals. The measured band gap in these curved regions is consistent with the direct band gap in MoS2 monolayers. The curved features near the edge terminals and the associated electronic properties may contribute to understanding catalytic behaviors of MoS2 nanostructures and have potential applications in future electronic devices and catalysts based on MoS2 nanostructures. Finally, we report a liquid-cell AFM study on the endosomal protein sorting process on the biological lipid membrane. The sorting mechanism relies on complex forming between Tom1 and the cargo sorting protein, Toll interacting protein (Tollip). The induced conformational change in Tollip triggers its dissociation from the lipid membrane and commitment to cargo trafficking. This collaborative study aims at characterizing the dynamic interaction between Tollip and the lipid membrane. To study this process we develop the liquid mode of AFM. We successfully demonstrate that Tollip is localized to the lipid membrane via association with PtdIns3P (PI(3)P), a major phospholipid in the cell membrane involved in protein trafficking. / Ph. D. / Two-dimensional (2D) materials are layered materials with thickness of single atom or few atoms. The ultimate thickness leads to novel properties that are useful for a wide range of applications in photovoltaics, electronics and quantum information. In order to explore these properties at the nanometer scale, we used scanning probe techniques, i.e., scanning tunneling microscopy (STM) and atomic force microscopy (AFM), to perform comprehensive investigations on these emerging materials. 2D materials, such as graphene and atomically thin transition-metal dichalcogenides (TMDCs), are promising candidates for building economic, safe and mechanically flexible solar cells with desirable optical and electronic properties, e.g. tunable sunlight absorption. The first part of the thesis focuses on graphene, a single-atom-thick carbon sheet. We deposited key components in organic solar cells, such as perylenetetracarboxylic dianhydride (PTCDA) and C₆₀ molecules, on graphene. On these materials we observed various novel nanostructures, like quasi-1D C₆₀ nanochains. The second part of the thesis focuses on mono- to few-layered MoS₂, which can be used as an active layer in high-efficiency solar cells. Our study has important implications in improving efficiency of organic solar cells in the future. In the final part of the thesis, we extended our subject to the biological lipid membrane, a 2D material critical in biology, and biophysical processes occurring on the membrane. Using a liquid-cell AFM, we investigated the endosomal protein sorting process on the biological membranes. Our study contributes to understanding of the interactions between the adaptor proteins and cell membranes in the protein sorting process that guides proteins to their proper destinations.