arXiv subjects

J. Kotakoski

Publications and source records attributed to J. Kotakoski.

13 recordsLinked to original sources

arXiv2026

Substrate-dependent pore formation in molybdenum disulfide monolayers under ion irradiation

Ion irradiation is a versatile tool for nanostructuring surfaces, yet the roles of energy deposition and dissipation at the surface and in ultrathin materials remain poorly understood. In this study, we investigate nanopore formation in monolayer MoS$_2$ on different substrates under irradiation of highly charged ions (HCIs) and swift heavy ions (SHIs): two types of ions that, despite having vastly different kinetic energies, interact primarily with the electronic system of the target. Using scanning transmission electron microscopy, we quantify pore radii and pore formation efficiencies for suspended MoS$_2$, MoS$_2$ on SiO$_2$, bilayer MoS$_2$ and MoS$_2$ on gold. Both pore size and pore formation efficiency exhibit a pronounced dependence on the type of substrate. Pores are largest and most frequent in MoS$_2$ on SiO$_2$, while the gold substrate massively quenches pore formation. The results indicate that the observed pore dimensions under both HCI and SHI irradiation are consistent with a central role of substrate and interface-dependent electronic dissipation pathways.

cond-mat.mtrl-sci↗

arXiv2023

Impurity atom configurations in diamond and their visibility via scanning transmission electron microscopy imaging

Dispersed impurities in diamond present a flourishing platform for research in quantum informatics, spintronics and single phonon emitters. Based on the vast pool of experimental and theoretical work describing impurity atoms in diamond, we review the configurations by the chemical element discussing the relevant atomic configurations and most important properties. Dopant structures expand from single to co-doping configurations, also combined with carbon vacancies. Despite of their importance, not much is known about the exact atomic configurations associated with the dopant structures beyond computational models, partially due to difficulties in their microscopic observation. To assess the visibility of these structures, we carry out image simulations to show that the heavier dopants may be easily discernible in scanning transmission electron microscopy annular dark field images, with a window of visibility of up to over $\pm$ 10 nm in defocus. We further present the first atomic resolution images of an impurity atom configuration (substitutional Er atom) in the diamond lattice, confirmed by a comparison to the simulated images. Overall, our results demonstrate that there is a vast research field waiting for the microscopy community in resolving the exact atomic structure of various impurity atom configurations in diamond.

cond-mat.mtrl-sci↗

arXiv2018

Nanopore fabrication and characterization by helium ion microscopy

The Helium Ion Microscope (HIM) has the capability to image small features with a resolution down to 0.35 nm due to its highly focused gas field ionization source and its small beam-sample interaction volume. In this work, the focused helium ion beam of a HIM is utilized to create nanopores with diameters down to 1.3 nm. It will be demonstrated that nanopores can be milled into silicon nitride, carbon nanomembranes (CNMs) and graphene with well-defined aspect ratio. To image and characterize the produced nanopores, helium ion microscopy and high resolution scanning transmission electron microscopy were used. The analysis of the nanopore's growth behavior, allows inferring on the profile of the helium ion beam.

physics.app-ph↗

arXiv2017

Manipulating low-dimensional materials down to the level of single atoms with electron irradiation

Recent advances in scanning transmission electron microscopy (STEM) instrumentation have made it possible to focus electron beams with sub-atomic precision and to identify the chemical structure of materials at the level of individual atoms. Here we discuss the dynamics that are observed in the structure of low-dimensional materials under electron irradiation, and the potential use of electron beams for single-atom manipulation. As a demonstration of the latter capability, we show how momentum transfer from the electrons of a 60-keV Ångström-sized STEM probe can be used to move silicon atoms embedded in the graphene lattice with atomic precision.

cond-mat.mtrl-sci↗

arXiv2017

Unraveling the 3D atomic structure of a suspended graphene/hBN van der Waals heterostructure

In this work we demonstrate that a free-standing van der Waals heterostructure, usually regarded as a flat object, can exhibit an intrinsic buckled atomic structure resulting from the interaction between two layers with a small lattice mismatch. We studied a freely suspended membrane of well aligned graphene on a hexagonal boron nitride (hBN) monolayer by transmission electron microscopy (TEM) and scanning TEM (STEM). We developed a detection method in the STEM that is capable of recording the direction of the scattered electron beam and that is extremely sensitive to the local stacking of atoms. Comparison between experimental data and simulated models shows that the heterostructure effectively bends in the out-of-plane direction, producing an undulated structure having a periodicity that matches the moiré wavelength. We attribute this rippling to the interlayer interaction and also show how this affects the intralayer strain in each layer.

cond-mat.mtrl-sci↗

arXiv2015

Towards weighing individual atoms by high-angle scattering of electrons

We consider theoretically the energy loss of electrons scattered to high angles when assuming that the primary beam can be limited to a single atom. We discuss the possibility of identifying the isotopes of light elements and of extracting information about phonons in this signal. The energy loss is related to the mass of the much heavier nucleus, and is spread out due to atomic vibrations. Importantly, while the width of the broadening is much larger than the energy separation of isotopes, only the shift in the peak positions must be detected if the beam is limited to a single atom. We conclude that the experimental case will be challenging but is not excluded by the physical principles as far as considered here. Moreover, the initial experiments demonstrate the separation of gold and carbon based on a signal that is related to their mass, rather than their atomic number.

physics.ins-det↗

arXiv2013

Structural manipulation of the graphene/metal-interface with Ar+ irradiation

Controlled defect creation is a prerequisite for the detailed study of disorder effects in materials. Here, we irradiate a graphene/Ir(111)-interface with low-energy Ar+ to study the induced structural changes. Combining computer simulations and scanning-probe microscopy, we show that the resulting disorder manifests mainly in the forms of intercalated metal adatoms and vacancy-type defects in graphene. One prominent feature at higher irradiation energies (from 1 keV up) is the formation of line-like depressions, which consist of sequential graphene defects created by the ion channeling within the interface -- much like a stone skipping on water. Lower energies result in simpler defects, down to 100 eV where more than one defect in every three is a graphene single vacancy.

cond-mat.mtrl-sci↗

arXiv2012

Ion irradiation tolerance of graphene as studied by atomistic simulations

As impermeable to gas molecules and at the same time transparent to high-energy ions, graphene has been suggested as a window material for separating a high-vacuum ion beam system from targets kept at ambient conditions. However, accumulation of irradiation-induced damage in the graphene membrane may give rise to its mechanical failure. Using atomistic simulations, we demonstrate that irradiated graphene even with a high vacancy concentration does not show signs of such instability, indicating a considerable robustness of graphene windows. We further show that upper and lower estimates for the irradiation damage in graphene can be set using a simple model.

cond-mat.mtrl-sci↗

arXiv2012

An accurate measurement of electron beam induced displacement cross sections for single-layer graphene

We present an accurate measurement and a quantitative analysis of electron-beam induced displacements of carbon atoms in single-layer graphene. We directly measure the atomic displacement ("knock-on") cross section by counting the lost atoms as a function of the electron beam energy and applied dose. Further, we separate knock-on damage (originating from the collision of the beam electrons with the nucleus of the target atom) from other radiation damage mechanisms (e.g. ionization damage or chemical etching) by the comparison of ordinary (12C) and heavy (13C) graphene. Our analysis shows that a static lattice approximation is not sufficient to describe knock-on damage in this material, while a very good agreement between calculated and experimental cross sections is obtained if lattice vibrations are taken into account.

cond-mat.mtrl-sci↗

arXiv2011

Stone-Wales--type transformations in carbon nanostructures driven by electron irradiation

Observations of topological defects associated with Stone-Wales-type transformations (i.e., bond rotations) in high resolution transmission electron microscopy (HRTEM) images of carbon nanostructures are at odds with the equilibrium thermodynamics of these systems. Here, by combining aberration-corrected HRTEM experiments and atomistic simulations, we show that such defects can be formed by single electron impacts, and remarkably, at electron energies below the threshold for atomic displacements. We further study the mechanisms of irradiation-driven bond rotations, and explain why electron irradiation at moderate electron energies (\sim100 keV) tends to amorphize rather than perforate graphene. We also show via simulations that Stone-Wales defects can appear in curved graphitic structures due to incomplete recombination of irradiation-induced Frenkel defects, similar to formation of Wigner-type defects in silicon.

cond-mat.mtrl-sci↗

arXiv2011

Cutting and controlled modification of graphene with ion beams

Using atomistic computer simulations, we study how ion irradiation can be used to alter the morphology of a graphene monolayer by introducing defects of specific type, and to cut graphene sheets. Based on the results of our analytical potential molecular dynamics simulations, a kinetic Monte Carlo code is developed for modelling morphological changes in a graphene monolayer under irradiation at macroscopic time scales. Impacts of He, Ne, Ar, Kr, Xe and Ga ions with kinetic energies ranging from tens of eV to 10 MeV and angles of incidence between 0\circ and 88\circ are studied. Our results provide microscopic insights into the response of graphene to ion irradiation and can directly be used for the optimization of graphene cutting and patterning with focused ion beams.

cond-mat.mtrl-sci↗

arXiv2011

Atomistic simulations of the implantation of low energy boron and nitrogen ions into graphene

By combining classical molecular dynamics simulations and density functional theory total energy calculations, we study the possibility of doping graphene with B/N atoms using low-energy ion irradiation. Our simulations show that the optimum irradiation energy is 50 eV with substitution probabilities of 55% for N and 40% for B. We further estimate probabilities for different defect configurations to appear under B/N ion irradiation. We analyze the processes responsible for defect production and report an effective swift chemical sputtering mechanism for N irradiation at low energies (~125 eV) which leads to production of single vacancies. Our results show that ion irradiation is a promising method for creating hybrid C-B/N structures for future applications in the realm of nanoelectronics.

cond-mat.mtrl-sci↗

arXiv2011

From Point Defects in Graphene to Two-Dimensional Amorphous Carbon

While crystalline two-dimensional materials have become an experimental reality during the past few years, an amorphous 2-D material has not been reported before. Here, using electron irradiation we create an sp2-hybridized one-atom-thick flat carbon membrane with a random arrangement of polygons, including four-membered carbon rings. We show how the transformation occurs step-by-step by nucleation and growth of low-energy multi-vacancy structures constructed of rotated hexagons and other polygons. Our observations, along with first-principles calculations, provide new insights to the bonding behavior of carbon and dynamics of defects in graphene. The created domains possess a band gap, which may open new possibilities for engineering graphene-based electronic devices.

cond-mat.mtrl-sci↗