arXiv subjects

Ondrej Dyck

Publications and source records attributed to Ondrej Dyck.

44 records · Page 3Linked to original sources

arXiv2018

Assembling Di- and Multiatomic Si Clusters in Graphene via Electron Beam Manipulation

We demonstrate assembly of di-, tri- and tetrameric Si clusters on the graphene surface using sub-atomically focused electron beam of a scanning transmission electron microscope. Here, an electron beam is used to introduce Si substitutional defects and defect clusters in graphene with spatial control of a few nanometers, and enable controlled motion of Si atoms. The Si substitutional defects are then further manipulated to form dimers, trimers and more complex structures. The dynamics of a beam induced atomic scale chemical process is captured in a time-series of images at atomic resolution. These studies suggest that control of the e-beam induced local processes offers the next step toward atom-by-atom nanofabrication and provides an enabling tool for study of atomic scale chemistry in 2D materials.

cond-mat.mtrl-sci↗

arXiv2018

Single atom force measurements: mapping potential energy landscapes via electron beam induced single atom dynamics

In the last decade, the atomically focused beam of a scanning transmission electron microscope (STEM) was shown to induce a broad set of transformations of material structure, open pathways for probing atomic-scale reactions and atom-by-atom matter assembly. However, the mechanisms of beam-induced transformations remain largely unknown, due to an extreme mismatch between the energy and time scales of electron passage through solids and atomic and molecular motion. Here, we demonstrate that a single dopant Si atom in the graphene lattice can be used as an atomic scale force sensor, providing information on the random force exerted by the beam on chemically-relevant time scales. Using stochastic reconstruction of molecular dynamic simulations, we recover the potential energy landscape of the atom and use it to determine the beam-induced effects in the thermal (i.e. white noise) approximation. We further demonstrate that the moving atom under beam excitation can be used to map potential energy along step edges, providing information about atomic-scale potentials in solids. These studies open the pathway for quantitative studies of beam-induced atomic dynamics, elementary mechanisms of solid-state transformations, and predictive atom-by-atom fabrication.

cond-mat.mtrl-sci↗

arXiv2018

Deep Learning of Atomically Resolved Scanning Transmission Electron Microscopy Images: Chemical Identification and Tracking Local Transformations

Recent advances in scanning transmission electron and scanning probe microscopies have opened exciting opportunities in probing the materials structural parameters and various functional properties in real space with angstrom-level precision. This progress has been accompanied by an exponential increase in the size and quality of datasets produced by microscopic and spectroscopic experimental techniques. These developments necessitate adequate methods for extracting relevant physical and chemical information from the large datasets, for which a priori information on the structures of various atomic configurations and lattice defects is limited or absent. Here we demonstrate an application of deep neural networks to extract information from atomically resolved images including location of the atomic species and type of defects. We develop a 'weakly-supervised' approach that uses information on the coordinates of all atomic species in the image, extracted via a deep neural network, to identify a rich variety of defects that are not part of an initial training set. We further apply our approach to interpret complex atomic and defect transformation, including switching between different coordination of silicon dopants in graphene as a function of time, formation of peculiar silicon dimer with mixed 3-fold and 4-fold coordination, and the motion of molecular 'rotor'. This deep learning based approach resembles logic of a human operator, but can be scaled leading to significant shift in the way of extracting and analyzing information from raw experimental data.

cond-mat.mtrl-sci↗

arXiv2018

Deep analytics of atomically-resolved images: manifest and latent features

Recent advances in scanning transmission electron and scanning tunneling microscopies allow researchers to measure materials structural and electronic properties, such as atomic displacements and charge density modulations, at an Angstrom scale in real space. At the same time, the ability to quickly acquire large, high-resolution datasets has created a challenge for rapid physics-based analysis of images that typically contain several hundreds to several thousand atomic units. Here we demonstrate a universal deep-learning based framework for locating and characterizing atomic species in the lattice, which can be applied to different types of atomically resolved measurements on different materials. Specifically, by inspecting and categorizing features in the output layer of a convolutional neural network, we are able to detect structural and electronic 'anomalies' associated with the presence of point defects in a tungsten disulfide monolayer, non-uniformity of the charge density distribution around specific lattice sites on the surface of strongly correlated oxides, and transition between different structural states of buckybowl molecules. We further extended our method towards tracking, from one image frame to another, minute distortions in the geometric shape of individual Si dumbbells in a 3-dimensional Si sample, which are associated with a motion of lattice defects and impurities. Due the applicability of our framework to both scanning tunneling microscopy and scanning transmission electron microscopy measurements, it can provide a fast and straightforward way towards creating a unified database of defect-property relationships from experimental data for each material.

cond-mat.mtrl-sci↗

arXiv2017

E-beam manipulation of Si atoms on graphene edges with aberration-corrected STEM

The burgeoning field of atomic level material control holds great promise for future breakthroughs in quantum and memristive device manufacture and fundamental studies of atomic-scale chemistry. Realization of atom-by atom control of matter represents a complex and ongoing challenge. Here, we explore the feasibility of controllable motion of dopant Si atoms at the edges of graphene via the sub-atomically focused electron beam in a scanning transmission electron microscope (STEM). We demonstrate that the graphene edges can be cleaned of Si atoms and then subsequently replenished from nearby source material. It is also shown how Si edge atoms may be pushed from the edge of a small hole into the bulk of the graphene lattice and from the bulk of the lattice back to the edge. This is accomplished through sputtering of the edge of the graphene lattice to bury or uncover Si dopant atoms. These experiments form an initial step toward general atomic scale material control.

cond-mat.mtrl-sci↗

arXiv2017

Mitigating E-beam-induced Hydrocarbon Deposition on Graphene for Atomic-Scale Scanning Transmission Electron Microscopy Studies

CVD grown graphene used in (scanning) transmission electron microscopy ((S)TEM) studies must undergo a careful transfer of the one-atom-thick membrane from the growth surface (typically a Cu foil) to the TEM grid. During this transfer process, the graphene invariably becomes contaminated with foreign material. This contamination proves to be very problematic in the (S)TEM because often >95% of the graphene is obscured and imaging of the pristine areas results in e-beam-induced hydrocarbon deposition which further acts to obscure the desired imaging area. In this article, we examine two cleaning techniques for CVD grown graphene that mitigate both aspects of the contamination problem: visible contamination covering the graphene, and invisible contamination that deposits onto the graphene under e-beam irradiation. The visible contamination may be removed quickly by a rapid thermal annealing to 1200 C in situ and the invisible e-beam-deposited contamination may be removed through an Ar/O2 annealing procedure prior to imaging in the (S)TEM.

cond-mat.mtrl-sci↗

arXiv2017

Two-Level Structural Sparsity Regularization for Identifying Lattices and Defects in Noisy Images

This paper presents a regularized regression model with a two-level structural sparsity penalty applied to locate individual atoms in a noisy scanning transmission electron microscopy image (STEM). In crystals, the locations of atoms is symmetric, condensed into a few lattice groups. Therefore, by identifying the underlying lattice in a given image, individual atoms can be accurately located. We propose to formulate the identification of the lattice groups as a sparse group selection problem. Furthermore, real atomic scale images contain defects and vacancies, so atomic identification based solely on a lattice group may result in false positives and false negatives. To minimize error, model includes an individual sparsity regularization in addition to the group sparsity for a within-group selection, which results in a regression model with a two-level sparsity regularization. We propose a modification of the group orthogonal matching pursuit (gOMP) algorithm with a thresholding step to solve the atom finding problem. The convergence and statistical analyses of the proposed algorithm are presented. The proposed algorithm is also evaluated through numerical experiments with simulated images. The applicability of the algorithm on determination of atom structures and identification of imaging distortions and atomic defects was demonstrated using three real STEM images. We believe this is an important step toward automatic phase identification and assignment with the advent of genomic databases for materials.

stat.AP↗

arXiv2017

Single atom manipulation and control in a scanning transmission electron microscope

We demonstrate that the sub-atomically focused beam of a scanning transmission electron microscope (STEM) can be used to controllably manipulate individual dopant atoms in a 2D graphene lattice. We demonstrate the manipulation of adsorbed source materials and the graphene lattice with the electron beam such that individual vacancy defects can be controllably passivated by Si substitutional atoms. We further demonstrate that these Si defects may be directed through the lattice via e-beam control or modified (as yet, uncontrollably) to form new defects which can incorporate new atoms into the graphene lattice. These studies demonstrate the potential of STEM for atom-by-atom nanofabrication and fundamental studies of chemical reactions in 2D materials on the atomic level.

cond-mat.mtrl-sci↗