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This study demonstrates that the nanopore terraces constructed on a multilayer graphene sheet could be employed to con-trol the conformation and transportation of an ssDNA for nanopore sequencing. As adsorbed on a terraced graphene na-nopore, the ssDNA has no in-plane swing nearby the nanopore, and can be locked on graphene terraces in a stretched con-formation. Under biasing, the accumulated ions near the nanopore promote the translocation of the locked ssDNA, and also disturb the balance between the driven force and resistance force acted on the nucleotide in pore. A critical force is found to be necessary in trigging the kickoff of the ssDNA translocation, implying an inherent field effect of the terraced graphene nanopore. By changing the intensities of electric field as trigger signal, the stop and go of an ssDNA in the nanopore are manipulated at single nucleobase level. The velocity of ssDNA in the nanopore can also be regulated by the frequency of the electro-stimulations. As a result, a new scheme of controllable translocation of ssDNA in graphene nanopores is realized by introducing controllers and triggers, appealing more explorations in experiment., Comment: 7 pages, 7 figures

Using molecular dynamics simulations, we investigated an integrated bio-nano interface consisting of a \b{eta}-sheet protein stacked onto graphene. We found that the stacking assembly of the model protein on graphene could be controlled by water molecules. The interlayer water filled within interstices of the bio-nano interface could suppress the molecular vibration of surface groups on protein, and could impair the CH...{\pi} interaction driving the attraction of the protein and graphene. The intermolecular coupling of interlayer water would be relaxed by the relative motion of protein upon graphene due to the interaction between water and protein surface. This effect reduced the hindrance of the interlayer water against the assembly of protein on graphene, resulting an appropriate adsorption status of protein on graphene with a deep free energy trap. Thereby, the confinement and the relative sliding between protein and graphene, the coupling of protein and water, and the interaction between graphene and water all have involved in the modulation of behaviors of water molecules within the bio-nano interface, governing the hindrance of interlayer water against the protein assembly on hydrophobic graphene. These results provide a deep insight into the fundamental mechanism of protein adsorption onto graphene surface in water., Comment: 29 pages and 7 figures

Extracting the sequence information of DNA from the blocked ionic current is the crucial step of the ionic current-based nanopore sequencing approaches. The thinnest graphene nanopore, which contained only one layer of carbon atoms, potentially has ultra-high DNA sequencing sensitivity. However, the dynamical translocation information of DNA contained in the blocked ionic current has not been well understood to date. In this letter, an assessment to the sensitivity of ionic current-based graphene nanopore DNA sensing approach was carried out using molecular dynamics simulations. By filtering the molecular thermal motion induced noise of ionic current, we found that the instantaneous conformational variations of DNA in graphene nanopore could be revealed from the fluctuations of the denoised ionic current. However, the blockage of ionic current which induced by the proximity of the DNA base-pairs to the nanopore (within 1.5 nm) was also observed. Although the expected single-base resolution of graphene nanopore should be enhanced by further studies, our findings indicated that the ionic current-based graphene nanopore sensing approach has high sensitivity to the instantaneous translocation status of DNA., Comment: 19 pages, 5figures

A computational investigation was carried out to understand the aggregation of nanoscale graphene with two typical assembly pathways of stacking assembly and sliding assembly in water. The interfacial-organized monolayer water film (MWF) hindering the aggregation of nanographene in both stacking and sliding assembly pathways was reported for the first time. By means of potential mean forces (PMFs) calculation, no energy barrier was observed during the sliding assembly of two graphene nanosheets, while the PMF profiles could be impacted by the contact forms of nanographene and the MWF within the interplate of two graphene nanosheets. To explore the potential physical basis of the hindering-role of self-organized interfacial water, the dynamical and structural properties as well as the status of hydrogen bonds (H-bonds) for interfacial water were investigated. We found that the compact, ordered structure and abundant H-bonds of the MWF could be taken as the fundamental aspects of the hindering-role of interfacial water for the hydrophobic assembly of nanographene. These findings are displaying a potential to further understand the hydrophobic assembly which mostly dominate the behaviors of nanomaterials, proteins etc. in aqueous solutions., Comment: 33 pages, 7 figures, 1 table

Graphene nanopore based sensor devices are exhibiting the great potential for the detection of DNA. To understand the fundamental aspects of DNA translocating through a graphene nanopore, in this work, molecular dynamics (MD) simulations and potential of mean force (PMF) calculations were carried out to investigate the layer impact of small graphene nanopore (2 nm-3 nm) to DNA translocation. It was observed that the ionic conductance was sensitive to graphene layer of open-nanopores, the probability for DNA translocation through graphene nanopore was related with the thickness of graphene nanopores. MD simulations showed that DNA translocation time was most sensitive to the thickness of graphene nanopore for a 2.4 nm aperture, and the observed free energy barrier of PMFs and the profile change revealed the increased retardation of DNA translocation through bilayer graphene nanopore as compared to monolayer graphene nanopore., Comment: 22 pages, 4 figures