The presence of defects in graphene has an essential influence on its physical and chemical properties. The formation, behaviour and healing of defects are determined by energetic characteristics of ...atomic scale structure changes. In this article, we review recent studies devoted to atomic scale reactions during thermally activated and irradiation-induced processes in graphene. The formation energies of vacancies, adatoms and topological defects are discussed. Defect formation, healing and migration are quantified in terms of activation energies (barriers) for thermally activated processes and by threshold energies for processes occurring under electron irradiation. The energetics of defects in the graphene interior and at the edge is analysed. The effects of applied strain and a close proximity of the edge on the energetics of atomic scale reactions are overviewed. Particular attention is given to problems where further studies are required.
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•Common vdW-functionals fail for some properties related to interlayer interaction.•PBE-D3(BJ) is the best for ground-state stackings of graphene and boron nitride.•vdW-DF2 is the ...best for modulus for axial compression and out-of-plane vibrations.•vdW-DF2 at the equilibrium interlayer distance is optimal for in-plane properties.•The PBE-D2 functional is improved for graphene by adjustment of the parameters.
Exchange-correlation functionals with corrections for van der Waals interactions (PBE-D2, PBE-D3, PBE-D3(BJ), PBE-TS, optPBE-vdW and vdW-DF2) are tested for graphene and hexagonal boron nitride, both in the form of bulk and bilayer. The characteristics of the potential energy surface, such as the barrier to relative sliding of the layers and magnitude of corrugation, and physically measurable properties associated with relative in-plane and out-of-plane motion of the layers including the shear modulus and modulus for axial compression, shear mode frequency and frequency of out-of-plane vibrations are considered. The PBE-D3(BJ) functional gives the best results for the stackings of hexagonal boron nitride and graphite that are known to be ground-state from the experimental studies. However, it fails to describe the order of metastable states of boron nitride in energy. The PBE-D3 and vdW-DF2 functionals, which reproduce this order correctly, are identified as the optimal choice for general studies. The vdW-DF2 functional is preferred for evaluation of the modulus for axial compression and frequency of out-of-plane vibrations, while the PBE-D3 functional is somewhat more accurate in calculations of the shear modulus and shear mode frequency. The best description of the latter properties, however, is achieved also using the vdW-DF2 functional combined with consideration of the experimental interlayer distance. In the specific case of graphene, the PBE-D2 functional works very well and can be further improved by adjustment of the parameters.
The analytical two-chain Frenkel-Kontorova model is used to describe domain wall networks in bilayer graphene upon biaxial stretching of one of the layers. We show that the ...commensurate-incommensurate phase transition leading to formation of a regular triangular domain wall network at the relative biaxial elongation of 3.0×10^{-3} is followed by the transition to another incommensurate phase with a striped network at the elongation of 3.7×10^{-3}. The reentrant transition to the phase with a triangular domain wall network is predicted for the elongation ∼10^{-2}.
An underlying mechanism for multi drug resistance (MDR) is up-regulation of the transmembrane ATP-binding cassette (ABC) transporter proteins. ABC transporters also determine the general fate and ...effect of pharmaceutical agents in the body. The three major types of ABC transporters are MDR1 (P-gp, P-glycoprotein, ABCB1), MRP1/2 (ABCC1/2) and BCRP/MXR (ABCG2) proteins. Flow cytometry (FCM) allows determination of the functional expression levels of ABC transporters in live cells, but most dyes used as indicators (rhodamine 123, DiOC(2)(3), calcein-AM) have limited applicability as they do not detect all three major types of ABC transporters. Dyes with broad coverage (such as doxorubicin, daunorubicin and mitoxantrone) lack sensitivity due to overall dimness and thus may yield a significant percentage of false negative results. We describe two novel fluorescent probes that are substrates for all three common types of ABC transporters and can serve as indicators of MDR in flow cytometry assays using live cells. The probes exhibit fast internalization, favorable uptake/efflux kinetics and high sensitivity of MDR detection, as established by multidrug resistance activity factor (MAF) values and Kolmogorov-Smirnov statistical analysis. Used in combination with general or specific inhibitors of ABC transporters, both dyes readily identify functional efflux and are capable of detecting small levels of efflux as well as defining the type of multidrug resistance. The assay can be applied to the screening of putative modulators of ABC transporters, facilitating rapid, reproducible, specific and relatively simple functional detection of ABC transporter activity, and ready implementation on widely available instruments.
The parameters of the triangular domain wall network in bilayer graphene with a simultaneously twisted and biaxially stretched bottom layer are studied using the two-chain Frenkel–Kontorova model. It ...is demonstrated that if the graphene layers are free to rotate, they prefer to stay co-aligned upon stretching the bottom layer, and the regular triangular network of tensile domain walls is formed upon the commensurate–incommensurate phase transition. If the angle between the layers is fixed, the regular triangular network of shear domain walls is observed at zero elongation of the bottom layer. Upon stretching the bottom layer, however, the domain walls transform into the tensile ones and the size of the commensurate domains decreases. We also show that the parameters of the isosceles triangular domain wall network in twisted bilayer graphene under shear strain can be determined through purely geometrical considerations. Experimental analysis of the orientation of domain walls and period of the triangular network would, on the one hand, contribute to understanding of the interlayer interaction of graphene layers and, on the other hand, serve for detection of relative strains and rotation between the layers. Vice versa, external strains can be used to control the parameters of the triangular domain wall network and, therefore, electronic properties of twisted bilayer graphene.
Healing of a hole in a carbon nanotube under electron irradiation in high-resolution transmission electron microscopy at room temperature is demonstrated using molecular dynamics simulations with the ...CompuTEM algorithm. Formation of an amorphous patch is observed in all simulation runs. The amorphous patch is formed in the absence of external carbon adatoms only via reconstruction of the carbon bond network. It consists mainly of 5-, 6-, and 7-membered rings and causes a small bottleneck. In addition, further growth of the initial amorphous patch under electron irradiation takes place. Two-coordinated atoms are found to play a crucial role in the latter process, analogous to autocatalysis of rearrangements of rings in fullerenes. The principal rearrangements in the presence of two-coordinated atoms can be described as generalized sp-defect migration: a bond is broken between two three-coordinated atoms, and one of them forms a new bond with a nearby two-coordinated atom. If the new and former two-coordinated atoms are not bonded, then the reaction leads both to displacement of the sp defect and changes in rings of the sp2 carbon structure. Migration by hopping of two-coordinated atoms and other reactions involving simultaneous breakage of two bonds are also detected but much rarely. Long-living two-coordinated atoms in the patch structure and related fast growth of the patch are observed in more than half of the simulation runs. Since the amorphous patch and bottleneck affect the electronic properties of the nanotube, such nanotubes can be a perspective for nanoelectronic applications.
We present a code modularization approach to design efficient and massively parallel cubic- and linear-scaling solvers for electronic structure calculations using atomic orbitals. The modular ...implementation of the orbital minimization method, in which linear algebra and parallelization issues are handled via external libraries, is demonstrated in the SIESTA code. The distributed block compressed sparse row (DBCSR) and scalable linear algebra package (ScaLAPACK) libraries are used for algebraic operations with sparse and dense matrices, respectively. The MatrixSwitch and libOMM libraries, recently developed within the Electronic Structure Library, facilitate switching between different matrix formats and implement the energy minimization. We show results comparing the performance of several cubic-scaling algorithms, and also demonstrate the parallel performance of the linear-scaling solvers, and their supremacy over the cubic-scaling solvers for insulating systems with sizes of several hundreds of atoms.
The method for production of atomic chains by heating of graphene nanoribbons (GNRs) is proposed and studied by molecular dynamics simulations. The Brenner potential is revised to adequately describe ...formation of atomic chains, edges and vacancy migration in graphene. A fundamentally different behaviour is observed for zigzag-edge GNRs with 3 and 4 atomic rows (3 and 4-ZGNRs) at 2500 K: formation of triple, double and single carbon chains with the length of hundreds of atoms in 3-ZGNRs and edge reconstruction with only short chains and GNR width reduction in 4-ZGNRs. The chain formation mechanism in 3-ZGNRs is revealed by analysis of bond reorganization reactions and is based on the interplay of two processes. The first one is breaking of bonds between 3 zigzag atomic rows leading to triple chain formation. The second one is bond breaking within the same zigzag atomic row, which occurs predominantly through generation of pentagons with subsequent bond breaking in pentagons and results in single or double chain formation. The DFT calculations of the barriers for relevant reactions are consistent with the mechanism proposed. The possibility of chain-based nanoelectronic devices with a controllable number of chains is discussed.
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The principal characteristics of interlayer interaction and relative motion of hexagonal boron nitride (h-BN) layers are investigated by the first-principles method taking into account van der Waals ...interactions. The dependence of the interlayer interaction energy on the relative translational displacement of h-BN layers (potential energy surfaces) are calculated for two relative orientations of the layers, namely, for the layers aligned in the same direction and in the opposite directions upon the relative rotation of the layers by 180 degrees. It is shown that the potential energy surfaces of bilayer h-BN can be approximated by the first Fourier components determined by symmetry. As a result, a wide set of physical quantities describing the relative motion of h-BN layers aligned in the same direction including barriers to their relative sliding and rotation, shear mode frequency and shear modulus are determined by a single parameter corresponding to the roughness of the potential energy surface, similar to bilayer graphene. The properties of h-BN layers aligned in the opposite directions are described by two such parameters. The possibility of partial and full dislocations in stacking of the layers is predicted for h-BN layers aligned in the same and opposite directions, respectively. The extended two-chain Frenkel-Kontorova model is used to estimate the width and formation energy of these dislocations on the basis of the calculated potential energy surfaces.
Properties of hexagonal boron nitride bilayer related to interlayer interaction (width and formation energy of dislocations, shear mode frequency,
etc.
) are estimated by approximation of potential energy surface by first Fourier harmonics.
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