No abstract

We describe the results of Brownian dynamics (BD) simulations of an atomic force microscope (AFM) tip scanned on locally suspended few-layer graphene. The effects of surface compliance and sample relaxation are directly related to the observed friction force. We demonstrate that the experimentally observed reduction of friction with an increasing number of graphene layers in case of a narrow scanning tip can be a result of decreased sample deformation energy due to increased local contact stiffness under the scanning tip. Simulations with varying scan rates indicate that surface relaxation at a given temperature can affect the frictional characteristics of atomically thin sheets in a manner not explained by conventional thermally activated models.

Using extensive room-temperature molecular dynamics simulations, we investigate selective aqueous cation trapping and permeation in graphene-embedded 18-crown-6 ether pores. We show that in the presence of suspended water-immersed crown-porous graphene, K ions rapidly organize and trap stably within the pores, in contrast with Na ions. As a result, significant qualitative differences in permeation between ionic species arise. The trapped ion occupancy and permeation behaviors are shown to be highly voltage-tunable. Interestingly, we demonstrate the possibility of performing conceptually straightforward ion-based logical operations resulting from controllable membrane charging by the trapped ions. In addition, we show that ionic transistors based on crown-porous graphene are possible, suggesting utility in cascaded ion-based logic circuitry. Our results indicate that in addition to numerous possible applications of graphene-embedded crown ether nanopores, including deionization, ion sensing/sieving, and energy storage, simple ion-based logical elements may prove promising as building blocks for reliable nanofluidic computational devices.

Since the discovery of the Amonton's law and with support of modern tribological models, friction between surfaces of three-dimensional materials is known to generally increase when the surfaces are in closer contact. Here, using molecular dynamics simulations of friction force microscopy on suspended graphene, we demonstrate an increase of friction when the scanning tip is retracted away from the sample. We explain the observed behavior and address why this phenomenon has not been observed for isotropic 3-D materials.

We propose a water-immersed nucleobase-functionalized suspended graphene nanoribbon as an intrinsically selective device for nucleotide detection. The proposed sensing method combines Watson-Crick selective base pairing with graphene's capacity for converting anisotropic lattice strain to changes in an electrical current at the nanoscale. Using detailed atomistic molecular dynamics (MD) simulations, we study sensor operation at ambient conditions. We combine simulated data with theoretical arguments to estimate the levels of measurable electrical signal variation in response to strains and determine that the proposed sensing mechanism shows significant promise for realistic DNA sensing devices without the need for advanced data processing, or highly restrictive operational conditions. 2 Fast, reliable, and cost-effective DNA sequencing continues to be an important open problem, as the vast majority of sequencing needs currently remains to be satisfied by the use of the Sanger method [1]. Despite the numerous advances made in automation and data analysis as part of the Human Genome Project [2, 3], the throughput rate and cost still significantly limit routine production of genomic data using the currently available technology.Various alternative approaches have been proposed, ranging from employing ionic current blockage by DNA nucleotides in aqueous nanopores [4, 5] to the use of chemically selective tunneling current probes [6]. Discovery of atomically thin carbon allotropes and their exceptional electronic, mechanical, and chemical properties has reinvigorated the search for nanoscale system based DNA sequencing methods in the past decade. Consequently, numerous graphene-based approaches have been proposed, mostly centered on the use of graphene as the ultimately thin membrane impermeable to water-dissolved ions [7][8][9][10] and nanoscale graphenebased field-effect transistor devices with nucleotide-specific electronic response [11][12][13][14][15]. In all proposed methods, robust single-measurement nucleobase selectivity in realistic measurement conditions naturally remains a fundamental challenge [16, 17]. with single nucleotide count errors of up to 90% [18], depending on the approach. In addition, device noise in ambient conditions remains one of the most serious problems in developing a robust graphene-based sensing methodology [12].Here, we report on utilizing graphene's electronic properties, effectively combined with the Watson-Crick base-pairing, as a possible method of high-speed DNA sequencing at ambient conditions in aqueous environment. The key feature of the proposed method is a graphene nanoribbon (GNR) with a nanoscale opening, the interior of which is chemically functionalized with selected nucleobases. As sketched in Fig. 1 (a), a single-strand DNA (ssDNA) molecule is 3 inserted into the functionalized pore and translocated at a prescribed rate perpendicularly to the GNR. When a base complementary to the GNR's functional group traverses the pore during translocation, selective hydro...