The spatial arrangement of target and probe molecules on the biosensor is a key aspect of the biointerface structure that ultimately determines the properties of interfacial molecular recognition and the performance of the biosensor. However, the spatial patterns of single molecules on practical biosensors have been unknown, making it difficult to rationally engineer biosensors. Here we have used high resolution atomic force microscopy to map closely spaced individual probes as well as discrete hybridization events on a functioning electrochemical DNA sensor surface. We also applied spatial statistical methods to characterize the spatial patterns at the single molecule level. We observed the emergence of heterogeneous spatiotemporal patterns of surface hybridization of hairpin probes. The clustering of target capture suggests that hybridization may be enhanced by proximity of probes and targets that are about 10 nm away. The unexpected enhancement was rationalized by the complex interplay between the nanoscale spatial organization of probe molecules, the conformational changes of the probe molecules, and target binding. Such molecular level knowledge may allow one to tailor the spatial patterns of the biosensor surfaces to improve the sensitivity and reproducibility.

Unlike supramolecular self-assembly methods that can organize many distinct components into designer shapes in a homogeneous solution (e.g., DNA origami), only relatively simple, symmetric structures consisting of a few distinct components have been self-assembled at solid surfaces. As the self-assembly process is confined to the surface/interface by mostly nonspecific attractive interactions, an open question is how these interfacial interactions affect multicomponent self-assembly. To gain a mechanistic understanding of the roles of surface environment in DNA origami self-assembly, here we studied the oligonucleotide-assisted folding of a long single-stranded DNA (ssDNA scaffold) that was end-tethered to a dynamic surface, which could actively regulate the DNA-surface interactions. The results showed that even weak surface attractions can lead to defective structures by inhibiting the merging of multiple domains into complete structures. A combination of surface anchoring and deliberate regulation of DNA-surface interactions allowed us to depart from the existing paradigm of surface confinement via nonspecific interactions and enabled DNA origami folding to proceed in a solution-like environment. Importantly, our strategy retains the key advantages of surface-mediated self-assembly. Moreover, surface-anchored oligonucleotides could sequence-specifically initiate the growth of DNA origamis of specific sizes and shapes. Our work enables information to be encoded into a surface and expressed into complex DNA surface architectures for potential nanoelectronics and nanophotonics applications. In addition, our approach to surface confinement may facilitate the 2D self-assembly of other molecular components, such as proteins, as maintaining conformational freedom may be a general challenge in the selfassembly of complex structures at surfaces.

Atomic force microscopy (AFM) can be used to measure surface properties at the nanoscale. However, interpretation of measurements from amplitude modulation AFM (AM-AFM) in liquid is not straightforward due to the interactions between the AFM tip, the surface being imaged, and the water. In this work, amplitude-distance measurements and molecular dynamics simulations of AM-AFM were employed to study the effect of surface chemistry on the amplitude of tip oscillation in water. The sample surfaces consisted of self-assembled monolayers where the hydrophilicity or hydrophobicity was determined by the terminal group of the alkanethiols. Analysis showed that surface chemical composition influences the hydration structure near the interface which affects the forces experienced by the tip and in turn changes the amplitude profile. This observation could aid our understanding of AM-AFM measurements of interfacial phenomena on various surfaces in water.

Self-assembled monolayers (SAMs) can reduce friction in boundary lubricated contacts by providing a low shear strength interface for sliding. However, the nanoscale mechanisms underlying low friction on SAMs are still not fully understood, especially in liquid environments in which hydrophobility or hydrophilicity affects friction. To understand this effect, friction of SAMs in water was measured using atomic force microscope experiments and molecular dynamics simulations, where hydrophilicity or hydrophobicity was determined by the terminal group of the alkanethiols. The friction on hydrophilic SAMs was larger than that on hydrophobic SAMs in both experiments and simulations, but this trend could not be explained by the strength of the adhesive force between the tip and the SAMs. Instead, analysis of the contributions of the water and SAMs to the total friction force revealed that the difference between the hydrophobic and hydrophilic SAMs could be explained by interactions between the tip and water during sliding. The much larger tip-water force on hydrophilic SAMs was attributed to a dense layer of water that was displaced during sliding as well as hydrogen bonds that formed between the water molecules and hydrophilic SAMs and then broken by the tip as it slid, leading to higher friction force.

The enthalpy and Gibbs free energy thermodynamical potentials of single walled carbon nanotubes were studied of all types (armchairs, zig-zags, chirals (n>m), and chiral (n