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Designing Topological Defects in 2D Materials Using Scanning Probe Microscopy and a Self-Healing Mechanism: a Density Functional-Based Molecular Dynamics Study

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Designing Topological Defects in 2D Materials Using Scanning Probe Microscopy and a Self-Healing Mechanism: a Density Functional-Based Molecular Dynamics Study Nanotechnology PAPER Related content - Elastic, plastic, and fracture mechanisms Designing topological defects in 2D materials in graphene materials Colin Daniels, Andrew Horning, Anthony using scanning probe microscopy and a self- Phillips et al. - Transforming graphene nanoribbons into healing mechanism: a density functional-based nanotubes by use of point defects A Sgouros, M M Sigalas, K Papagelis et molecular dynamics study al. - Theoretical study of carbon-based tips for scanning tunnelling microscopy To cite this article: Igor Popov et al 2017 Nanotechnology 28 495706 C González, E Abad, Y J Dappe et al. Recent citations View the article online for updates and enhancements. - Reducing sheet resistance of self- assembled transparent graphene films by defect patching and doping with UV/ozone treatment Tijana Tomaševi-Ili et al - Nanopatterning on calixarene thin films via low-energy field-emission scanning probe lithography Xiaoyue He et al This content was downloaded from IP address 128.194.154.59 on 26/07/2018 at 00:41 Nanotechnology Nanotechnology 28 (2017) 495706 (8pp) https://doi.org/10.1088/1361-6528/aa9679 Designing topological defects in 2D materials using scanning probe microscopy and a self-healing mechanism: a density functional-based molecular dynamics study Igor Popov1,2 , Ivana Đurišić2 and Milivoj R Belić3 1 Institute for Multidisciplinary Research, University of Belgrade, Kneza Višeslava 1, 11030 Belgrade, Serbia 2 Institute of Physics Belgrade, University of Belgrade, Pregrevica 118, 11080 Belgrade, Serbia 3 Science Program, Texas A & M University at Qatar, P.O. Box 23874, Qatar E-mail: [email protected] Received 23 August 2017, revised 25 October 2017 Accepted for publication 27 October 2017 Published 15 November 2017 Abstract Engineering of materials at the atomic level is one of the most important aims of nanotechnology. The unprecedented ability of scanning probe microscopy to address individual atoms opened up the possibilities for nanomanipulation and nanolitography of surfaces and later on of two-dimensional materials. While the state-of-the-art scanning probe lithographic methods include, primarily, adsorption, desorption and repositioning of adatoms and molecules on substrates or tailoring nanoribbons by etching of trenches, the precise modification of the intrinsic atomic structure of materials is yet to be advanced. Here we introduce a new concept, scanning probe microscopy with a rotating tip, for engineering of the atomic structure of membranes based on two-dimensional materials. In order to indicate the viability of the concept, we present our theoretical research, which includes atomistic modeling, molecular dynamics simulations, Fourier analysis and electronic transport calculations. While stretching can be employed for fabrication of atomic chains only, our comprehensive molecular dynamics simulations indicate that nanomanipulation by scanning probe microscopy with a rotating tip is capable of assembling a wide range of topological defects in two-dimensional materials in a rather controllable and reproducible manner. We analyze two possibilities. In the first case the probe tip is retracted from the membrane while in the second case the tip is released beneath the membrane allowing graphene to freely relax and self-heal the pore made by the tip. The former approach with the tip rotation can be achieved experimentally by rotation of the sample, which is equivalent to rotation of the tip, whereas irradiation of the membrane by nanoclusters can be utilized for the latter approach. The latter one has the potential to yield a yet richer diversity of topological defects on account of a lesser determinacy. If successfully realized experimentally the concept proposed here could be an important step toward controllable nanostructuring of two-dimensional materials. Keywords: graphene membrane, atomic structure, nanostructuring, topological defects, molecular dynamics, scanning probe methods (Some figures may appear in colour only in the online journal) 0957-4484/17/495706+08$33.00 1 © 2017 IOP Publishing Ltd Printed in the UK Nanotechnology 28 (2017) 495706 I Popov et al 1. Introduction graphene by this method but with supersonic microclusters has been recently demonstrated [24]. Precise, accurate and predictable nanostructuring is an ulti- mate goal of nanophysics and nanotechnology. Scanning probe microscopy (SPM) including scanning tunneling 2. Method microscopy (STM) [1] and atomic force microscopy (AFM) [2] have proven records of their capabilities for nanos- We employed the density functional-based tight binding tructuring (i.e. scanning probe nanostructuring—SPN) at the (DFTB) method [25, 26] as implemented in DFTB+ code nanometer level. Impressive precision has already been [27]. The method has a proven record in the research of demonstrated by Eigler in 1989 who manipulated 35 indivi- plastic deformations of graphene, including our reports on the dual xenon atoms on a nickel substrate [3]. The first nanos- breaking of graphene nanoribbons under extreme uniaxial tructuring demonstration was followed by nanoscale stresses [28–30]. We performed geometry optimizations, patterning of a H-passivated Si(100) surface by STM [4], molecular dynamics (MD) simulations and electronic trans- which paved the way for using STM as a tool in lithography port calculations within a Γ-point approximation. The initial processes [5]. The focus of research in SPN techniques has geometries prior to MD simulations were fully relaxed by been mainly on adsorption, desorption and manipulation of conjugate gradient optimization where the maximal force on adatomic and molecular decorations of substrates [6–11]. − atoms was smaller than 0.04 eV Å 1. Van der Waals inter- Local anodic oxidation [12, 13] is also often utilized, which action was included in calculations. Conductance of the sys- can provide a spatially controlled modification of various tems was obtained by DFTB augmented by Green’s functions materials including graphene sheets [14]. Complex structures [31], whereas the Landauer–Buttiker [32] formula was uti- with lithographic resolutions down to 25 nm have been lized for calculations of electronic current. demonstrated using the AFM method [15, 16], whereas much We investigated the mechanism of piercing of suspended higher spatial resolutions down to 2.5 nm have been achieved graphene using an atomically sharp STM tip within the by STM in the fabrication of graphene nanoribbons with the supercell approach. The length of the supercell was 4.92nm desired crystallographic orientations [17]. The thermo- along the armchair direction of graphene and 5.11nm along chemical nanolithography technique has also been presented its zig-zag direction. The whole supercell contained 960 as a promising SPN–AFM method [18]. carbon (C) atoms and 120 gold (Au) atoms (figure 1(a)). The Here we introduce a conceptually new approach to SPN: tip consisted of face-centered cubic Au crystal with a pyr- utilization of SPM with a rotating tip as an additional degree amidal geometry. The tip apex was made of a single Au atom. of freedom. Using atomistic modeling, density functional- The sides of the pyramid corresponded to the stable Au(111) based molecular dynamics simulations, and Fourier analysis surfaces, as shown in figure 1(a). The existence of pyramidal we demonstrate this concept with the engineering of topolo- golden nanoclusters has been reported before [33]. We chose gical defects in a suspended graphene membrane, whereas the gold for the tip material since, as a noble metal, it does not method is transferable to the larger class of two-dimensional strongly chemically interact with other materials, including (2D) materials. Defects have important roles in the properties graphene. In order to isolate the effects of the tip on graphene of graphene and other 2D materials [19, 20] hence large effort from eventual changes of tip geometry we did not allow Au has been invested in understanding their effects, detection, atoms to relax during the simulations, essentially simulating elimination or utilization in the engineering of the desired an ideally rigid tip. The approximation was adequate for material properties [21, 22]. Our simulations indicate that a proving the concept while other weakly reactive tips, stronger choice of a material for the scanning probe tip, which does not than the target 2D material, should be utilized in real strongly chemically interact with the graphene, allows experiment. rebinding of carbon atoms based primarily on positions of the atoms relative to the nearest atomic neighbors of the tip. Rotation of the tip presents an additional degree of freedom to the standard SPM, which can provide a finer precision 3. Results and discussion necessary to achieve the desired relative positioning of the tip and carbon neighbors. Note that one can rotate the membrane The drilling started with the tip apex initially positioned rather than the tip to achieve the same effect, since only above one of the three high-symmetry sites of graphene: the relative positions matter. Application of STM on a rotating center of a phenyl ring (hollow site), on the top of a carbon sample has already been experimentally demonstrated [23].In atom (top site) or at the middle of a C–C bond (bridge site). the second part of the manuscript we analyze the possibility of The suspension of graphene is simulated by fixing C atoms engineering topological defects by the self-healing mech- that encompass two rows of phenyl rings at each edge of the anism upon instant removal of the tip from the graphene simulated membrane. The starting position of the tip apex is membrane after the tip has penetrated the membrane up to 2Åabove the graphene. We optimized all initial geometries certain depths. This approach can also be realized in an prior to MD simulations using the conjugate gradient method. equivalent experiment with a similar effect, for example by The tip–graphene repulsion caused a shallow sag in the gra- irradiation of the graphene membrane by energetic nanoscale phene with maximal departure of C atoms by 1.01 Åfrom the clusters. The experimental feasibility of generating defects in basal graphene plane (i.e. fixed C atoms).
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