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.