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We have investigated the influence of electron beam generated defects on the structure of periodic lattice distortions (PLDs) which accompany charge density wave modulations in $1T\text{\ensuremath{-}}\mathrm{Ta}{\mathrm{S}}_{2}$ and $1T\text{\ensuremath{-}}\mathrm{TaS}{\mathrm{e}}_{2}$. Lattice defects were generated through irradiation with high-energy electrons in a transmission electron microscope (TEM). Using atomically resolved high-resolution TEM imaging, we investigate the PLD structure and the changes in this structure with prolonged exposure to the electron beam. We observe the formation of dislocationlike topological defects in the PLD structure. Prolonged exposure to the electron beam also leads to an increase in density of these defects. This is also accompanied by an increase in structural disorder of the PLD. Density functional theory calculations were also performed in order to understand sulfur (S) and selenium (Se) vacancy defect formation in $1T\text{\ensuremath{-}}\mathrm{TaS}{\mathrm{e}}_{2}$ and $1T\text{\ensuremath{-}}\mathrm{Ta}{\mathrm{S}}_{2}$ and their effects on the PLD structure. The formation energy of Se/S vacancies was calculated to be lowest for the highly displaced S/Se atoms in the vicinity of PLD maxima. Vacancies formed at the less displaced sites near the PLD minima were found to have lower formation energy. The calculations also showed that an increase in the S/Se vacancies leads to the formation of dislocations and an increase in disorder in the PLD structures. This supports the experimental observations.

We theoretically study the atomic structure and energetics of silicon and silicon-nitrogen impurities in graphene. Using density-functional theory, we get insight into the atomic structures of the impurities, evaluate their formation energies and assess their abundance in realistic samples. We find that nitrogen, as well as oxygen and hydrogen, are trapped at silicon impurities, considerably altering the electronic properties of the system. Furthermore, we show that nitrogen doping can induce local magnetic moments resulting in spin-dependent transport properties, even though neither silicon nor nitrogen impurities are magnetic by themselves. To simulate large systems with many randomly distributed impurities, we derive tight-binding models that describe the effects of the impurities on graphene {\pi} electron structure. Then by using the linear-scaling real-space Kubo-Greenwood method, we evaluate the transport properties of large-scale systems with random distribution of impurities, and find the fingerprint-like scattering cross sections for each impurity type. The transport properties vary widely, and our results indicate that some of the impurities can even induce strong localization in realistic graphene samples., Comment: 17 pages, 9 figures

Motivated by recent in situ studies of carbon nanotube growth from large transition-metal nanoparticles, we study various $\ensuremath{\alpha}$-iron (ferrite) facets at different carbon concentrations using ab initio methods. The studied (110), (100), and (111) facets show qualitatively different behavior when carbon concentration changes. In particular, adsorbed carbon atoms repel each other on the (110) facet, resulting in carbon dimer and graphitic material formation. Carbon on the (100) facet forms stable structures at concentrations of about 0.5 monolayer and at 1.0 monolayer this facet becomes unstable due to a frustration of the top-layer iron atoms. The stability of the (111) facet is weakly affected by the amount of adsorbed carbon and its stability increases further with respect to the (100) facet with increasing carbon concentration. The exchange of carbon atoms between the surface and subsurface regions on the (111) facet is easier than on the other facets and the formation of carbon dimers is exothermic. These findings are in accordance with a recent in situ experimental study where the existence of graphene-decorated (111) facets is related to increased carbon concentration.

Using x-ray photoelectron spectroscopy, thermal desorption spectroscopy, and scanning tunneling microscopy, we show that upon keV Xe+ irradiation of graphene on Ir(111), Xe atoms are trapped under the graphene. Upon annealing, aggregation of Xe leads to graphene bulges and blisters. The efficient trapping is an unexpected and remarkable phenomenon given the absence of chemical binding of Xe to Ir and to graphene, the weak interaction of a perfect graphene layer with Ir(111), as well as the substantial damage to graphene due to irradiation. By combining molecular dynamics simulations and density functional theory calculations with our experiments, we uncover the mechanism of trapping. We describe ways to avoid blister formation during graphene growth, and also demonstrate how ion implantation can be used to intentionally create blisters without introducing damage to the graphene layer. Our approach may provide a pathway to synthesize new materials at a substrate-2D material interface or to enable confined reactions at high pressures and temperatures. (Less)

By combining high-resolution transmission electron microscopy experiments and first-principles calculations, we study production, diffusion, and agglomeration of sulfur vacancies in monolayer MoS${}_{2}$ under electron irradiation. Single vacancies are found to be mobile under the electron beam and tend to agglomerate into lines. Different kinds of such extended defects are identified in the experiments, and their atomic structures and electronic properties are determined with the help of calculations. The orientation of line defects is found to be sensitive to mechanical strain. Our calculations also indicate that the electronic properties of the extended defects can be tuned by filling vacancy lines with other atomic species, thereby suggesting a way for strain and electron-beam-assisted engineering of MoS${}_{2}$-based nanostructures.

We calculate from first principles the electronic structure and optical properties of a number of transition metal dichalcogenide (TMD) bilayer heterostructures consisting of MoS2 layers sandwiched with WS2, MoSe2, MoTe2, BN, or graphene sheets. Contrary to previous works, the systems are constructed in such a way that the unstrained lattice constants of the constituent incommensurate monolayers are retained. We find strong interaction between the \Gamma-point states in all TMD/TMD heterostructures, which can lead to an indirect gap. On the other hand, states near the K-point remain as in the monolayers. When TMDs are paired with BN or graphene layers, the interaction around \Gamma-point is negligible, and the electronic structure resembles that of two independent monolayers. Calculations of optical properties of the MoS2/WS2 system show that even when the valence and conduction band edges are located in different layers, the mixing of optical transitions is minimal, and the optical characteristics of the monolayers are largely retained in these heterostructures. The intensity of interlayer transitions is found to be negligibly small, a discouraging result for engineering the optical gap of TMDs by heterostructuring., Comment: 7 pages, 7 figures; Title changed to match published version

Using $GW$ first-principles calculations for few-layer and bulk MoS${}_{2}$, we study the effects of quantum confinement on the electronic structure of this layered material. By solving the Bethe-Salpeter equation, we also evaluate the exciton energy in these systems. Our results are in excellent agreement with the available experimental data. Exciton binding energy is found to dramatically increase from 0.1 eV in the bulk to 1.1 eV in the monolayer. The fundamental band gap increases as well, so that the optical transition energies remain nearly constant. We also demonstrate that environments with different dielectric constants have a profound effect on the electronic structure of the monolayer. Our results can be used for engineering the electronic properties of MoS${}_{2}$ and other transition-metal dichalcogenides and may explain the experimentally observed variations in the mobility of monolayer MoS${}_{2}$.

Using density-functional theory calculations, we studied the electronic and magnetic properties of zigzag graphene nanoribbons (ZGNRs) with gold (Au) atoms embedded into different sites of the ZGNRs. Strong site dependence was found, and the system had the ferromagnetic or antiferromagnetic ground state depending on the Au atom position. Spin gapless semiconductor (SGS) behavior was observed when the Au atom was embedded into the center and edge sites of the ZGNRs. The simulations showed that the electronic structure of the ribbon strongly depends on ZGNR width, but the SGS behavior is always present when the Au atom is embedded into the center and edge sites. The SGS properties were also found to be dependent on impurity atom concentration, so that they can be tuned by either selecting the proper positions of Au atoms or changing their concentration. Our results suggest a flexible way of designing SGSs, which could be used in various spintronic, electronic, and optoelectronic applications.

We combine first-principles molecular-dynamics simulations with high-resolution transmission electron microscopy experiments to draw a detailed microscopic picture of irradiation effects in hexagonal boron nitride ($h$-BN) monolayers. We determine the displacement threshold energies for boron and nitrogen atoms in $h$-BN, which differ significantly from the tight-binding estimates found in the literature and remove ambiguity from the interpretation of the experimental results. We further develop a kinetic Monte Carlo model which allows to extend the simulations to macroscopic time scales and make a direct comparison between theory and experiments. Our results provide a comprehensive picture of the response of $h$-BN nanostructures to electron irradiation.

By combining analytical molecular-dynamics with density-functional theory simulations, we study the radiation hardness of mechanically strained low-dimensional nanosystems such as carbon nanotubes, graphene, and Si nanowires. We show that the radiation hardness of all these structures decreases with strain but the effect is most pronounced in nanowire due to the bulk structure of its core in contrast with the planar structure of nanotubes and graphene. Our results not only elucidate the microscopic mechanism of irradiation-induced defect production in strained nanomaterials but also provide quantitative information required for assessing the stability of nanocomponents in composite materials subjected to mechanical strain and irradiation, e.g., in space applications.

Using atomistic computer simulations based on analytical potential and density-functional theory models, we study effects of ion irradiation on graphene. We identify the types and concentrations of defects which appear in graphene under impacts of various ions with energies ranging from tens of electron volts to mega-electron volts. For two-dimensional targets, defects beyond single and double vacancies are formed via in-plane recoils. We demonstrate that the conventional approach based on binary-collision approximation and stochastic algorithms developed for bulk solids cannot be applied to graphene and other low-dimensional systems. Finally, taking into account the gas-holding capacity of graphene, we suggest the use of graphene as the ultimate membrane for ion-beam analysis of gases and other volatile systems which cannot be put in the high vacuum required for the operation of ion beams.

Local controllable modification of the electronic structure of carbon nanomaterials is important for the development of carbon-based nanoelectronics. By combining density-functional theory simulations with Ar-ion-irradiation experiments and low-temperature scanning tunneling microscopy and spectroscopy (STM/STS) characterization of the irradiated samples, we study the changes in the electronic structure of single-walled carbon nanotubes due to the impacts of energetic ions. As nearly all irradiation-induced defects look as nondistinctive hillocklike features in the STM images, we compare the experimentally measured STS spectra to the computed local density of states of the most typical defects with an aim to identify the type of defects and assess their abundance and effects on the local electronic structure. We show that individual irradiation-induced defects can give rise to single and multiple peaks in the band gap of the semiconducting nanotubes and that a similar effect can be achieved when several defects are close to each other. We further study the stability of defects and their evolution during STM measurements. Our results not only shed light on the abundance of the irradiation-induced defects in carbon nanotubes and their signatures in STS spectra but also suggest a way the STM can be used for engineering the local electronic structure of defected carbon nanotubes.

The presence of vacancy clusters in carbon nanotubes has been assumed to explain the formation of carbon peapods and the difference between the experimentally measured and theoretical fracture strength of nanotubes. We use atomistic simulations at various levels of theory to study the characteristics of large vacancies formed by up to six missing atoms. We show that the formation of big ``holes'' on nanotube walls is energetically unfavorable as the vacancies tend to split into smaller defects due to the reconstruction of the nanotube atomic network. We also demonstrate that there is a weak but long-ranged interaction between the vacancies not only through strain fields but, surprisingly, also due to electronic effects, similar to those of adatoms on metal surfaces.

As recent experiments demonstrate, the inner shells of multiwalled carbon nanotubes are more sensitive to electron irradiation than the outer shells. To understand the origin of such counterintuitive behavior, we employ a density-functional-theory based tight-binding method and calculate the displacement threshold energies for carbon atoms in single-walled nanotubes with different diameters and chiralities. We show that the displacement energy and the defect production rate strongly depend on the diameter of the nanotube and its chirality, with the displacement energy being lower, but saturating towards the value for graphite when the tube diameter increases. This implies that the threshold electron energies to produce damage in nanotubes with diameters smaller than 1nm are less than the commonly accepted value for graphitic nanoparticles. We also calculate the displacement energies for carbon atoms near defects and show that if a single vacancy is formed, it will likely be transformed to a double vacancy, as the nanotube atomic network with double vacancies has no energetically unfavorable undercoordinated atoms.

The production and migration of carbon interstitials in carbon nanotubes under electron irradiation is studied experimentally and theoretically. It is shown that the threshold for displacing carbon atoms and the defect production rate strongly depend on the diameter of the nanotubes. Multiwalled nanotubes shrink by a loss of atoms and by diffusion of interstitials through the inner hollow in the axial direction. Thus, experimental evidence is given that nanotubes can act as nanoscale pipes for the transport of atoms.

We perform molecular dynamics simulations to study motion of heavy ions with kilo-electron-volt energies through multiwalled carbon nanotubes. We show that under certain conditions on the tube alignment with respect to the ion beam and on ion energies, the ions can efficiently channel through the empty cores of the nanotubes. We demonstrate that the dependence of the critical angle on ion energy obeys a simple continuum-theory-based equation. We further discuss making a nanotube-based conduit for energetic ions, which should work as an aperture and allow one to manipulate ion beams at the nanoscale.

Ultra-low friction between shells of multiwalled carbon nanotubes indicates that, when the nanotubes are used as reinforcement agents, the mechanical load is carried by the outermost shell of the tube only. We suggest using small-dose electron or ion irradiation to partially transfer the load to the nanotube inner shells. Employing analytical potential molecular dynamics, we simulate the response of multiwalled nanotubes to an external force acting on one of the shells with irradiation-induced defects which bridge adjacent shells. We demonstrate that a small number of defects can increase the interlayer shear strength by several orders of magnitude. We further discuss how the irradiation-induced load transfer can be measured experimentally and how, by manipulating the particle beam characteristics, one can improve the load transfer between preselected shells.

We employ density-functional plane-wave ab initio and tight-binding methods to study the adsorption and migration of carbon adatoms on single-walled carbon nanotubes. We show that the adatom adsorption and migration energies strongly depend on the nanotube diameter and chirality, which makes the model of the carbon adatom on a flat graphene sheet inappropriate. Calculated migration energies for the adatoms agree well with the activation energies obtained from experiments on annealing of irradiation damage in single-walled nanotubes and attributed to single carbon interstitials.

Recent experiments on irradiated carbon nanotubes provide evidence that ion bombardment gives rise to nanotube amorphization and dramatic dimensional changes. Using an empirical potential along with molecular dynamics, we study structure and formation probabilities of atomic-scale defects produced by low-dose irradiation of nanotubes with Ar ions. For this, we simulate impact events over a wide energy range of incident ions. We show that the maximum damage production occurs for a bombarding ion energy of about 600 eV, and that the most common defects produced at all energies are vacancies, which at low temperatures are metastable but long-lived defects. Employing the tight-binding Green's function technique, we also calculate scanning tunneling microscopy (STM) images of irradiated nanotubes. We demonstrate that irradiation-induced defects may be detected by STM and that isolated vacancies may look like bright spots in atomically resolved STM images of irradiated nanotubes.

Department of Applied Physics, Aalto University,P.O. Box 1100, 00076 Helsinki, Finland(Dated: February 4, 2011)By combining classical molecular dynamics simulations and density functional theory total en-ergy calculations, we study the possibility of doping graphene with B/N atoms using low-energyion irradiation. Our simulations show that the optimum irradiation energy is 50 eV with substi-tution probabilities of 55% for N and 40% for B. We further estimate probabilities for differentdefect configurations to appear under B/N ion irradiation. We analyze the processes responsiblefor defect production and report an effective swift chemical sputtering mechanism for N irradiationat low energies (∼125 eV) which leads to production of single vacancies. Our results show that ionirradiation is a promising method for creating hybrid C-B/N structures for future applications inthe realm of nanoelectronics.

The migration of gold atoms attached to single vacancies near the edges of graphene ribbons is studied using density-functional theory calculations. The stable position for a single gold atom is found to be on top of a vacancy, as in an infinite graphene sheet. An energy of 5 eV is needed for the Au atom to move through the vacancy to the other side of the sheet, but the Au atom can migrate in lateral direction together with the vacancy, with a migration barrier of about 2.2 eV. The sites near the edges of the graphene layer are energetically more favorable for gold-atom-vacancy pairs than sites in the middle of extended graphene layers. The migration barriers for different pathways show that it is easier for the gold atom to move toward the edge where it can be captured. When the gold atom reaches the edge, it can migrate along the edge with an energy barrier of only 1.4 eV. Our results explain recent experimental observations [Y. Gan , Small 4, 587 (2008)] and provide information on the dynamics of metal atoms on substitutional sites in graphene as well as on their agglomeration at defects and at edges of graphene ribbons.