Jani Kotakoski

Bio: Jani Kotakoski is an academic researcher from University of Vienna. The author has contributed to research in topics: Graphene & Scanning transmission electron microscopy. The author has an hindex of 45, co-authored 174 publications receiving 10842 citations. Previous affiliations of Jani Kotakoski include Technische Universität Darmstadt & Tel Aviv University.

Structural defects in graphene

Abstract: Graphene is one of the most promising materials in nanotechnology. The electronic and mechanical properties of graphene samples with high perfection of the atomic lattice are outstanding, but structural defects, which may appear during growth or processing, deteriorate the performance of graphene-based devices. However, deviations from perfection can be useful in some applications, as they make it possible to tailor the local properties of graphene and to achieve new functionalities. In this article, the present knowledge about point and line defects in graphene are reviewed. Particular emphasis is put on the unique ability of graphene to reconstruct its lattice around intrinsic defects, leading to interesting effects and potential applications. Extrinsic defects such as foreign atoms which are of equally high importance for designing graphene-based devices with dedicated properties are also discussed.

Two-dimensional transition metal dichalcogenides under electron irradiation: defect production and doping.

Abstract: Using first-principles atomistic simulations, we study the response of atomically thin layers of transition metal dichalcogenides (TMDs)--a new class of two-dimensional inorganic materials with unique electronic properties--to electron irradiation. We calculate displacement threshold energies for atoms in 21 different compounds and estimate the corresponding electron energies required to produce defects. For a representative structure of MoS2, we carry out high-resolution transmission electron microscopy experiments and validate our theoretical predictions via observations of vacancy formation under exposure to an 80 keV electron beam. We further show that TMDs can be doped by filling the vacancies created by the electron beam with impurity atoms. Thereby, our results not only shed light on the radiation response of a system with reduced dimensionality, but also suggest new ways for engineering the electronic structure of TMDs.

From point defects in graphene to two-dimensional amorphous carbon.

Abstract: While crystalline two-dimensional materials have become an experimental reality during the past few years, an amorphous 2D material has not been reported before. Here, using electron irradiation we create an $s{p}^{2}$-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 multivacancy 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.

Accurate measurement of electron beam induced displacement cross sections for single-layer graphene.

Abstract: 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 ($^{12}\mathrm{C}$) and heavy ($^{13}\mathrm{C}$) 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.

Effects of ion bombardment on a two-dimensional target: Atomistic simulations of graphene irradiation

Abstract: 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.

Fast parallel algorithms for short-range molecular dynamics

Abstract: Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

Structural defects in graphene

Abstract: Graphene is one of the most promising materials in nanotechnology. The electronic and mechanical properties of graphene samples with high perfection of the atomic lattice are outstanding, but structural defects, which may appear during growth or processing, deteriorate the performance of graphene-based devices. However, deviations from perfection can be useful in some applications, as they make it possible to tailor the local properties of graphene and to achieve new functionalities. In this article, the present knowledge about point and line defects in graphene are reviewed. Particular emphasis is put on the unique ability of graphene to reconstruct its lattice around intrinsic defects, leading to interesting effects and potential applications. Extrinsic defects such as foreign atoms which are of equally high importance for designing graphene-based devices with dedicated properties are also discussed.

Science and technology roadmap for graphene, related two-dimensional crystals, and hybrid systems

Abstract: We present the science and technology roadmap for graphene, related two-dimensional crystals, and hybrid systems, targeting an evolution in technology, that might lead to impacts and benefits reaching into most areas of society. This roadmap was developed within the framework of the European Graphene Flagship and outlines the main targets and research areas as best understood at the start of this ambitious project. We provide an overview of the key aspects of graphene and related materials (GRMs), ranging from fundamental research challenges to a variety of applications in a large number of sectors, highlighting the steps necessary to take GRMs from a state of raw potential to a point where they might revolutionize multiple industries. We also define an extensive list of acronyms in an effort to standardize the nomenclature in this emerging field.