arXiv subjects

Tatiana Latychevskaia

Publications and source records attributed to Tatiana Latychevskaia.

At least 37 records · Page 2Linked to original sources

arXiv2019

Direct visualization of charge transport in suspended (or free-standing) DNA strands by low-energy electron microscopy

Low-energy electrons offer a unique possibility for long exposure imaging of individual biomolecules without significant radiation damage. In addition, low-energy electrons exhibit high sensitivity to local potentials and thus can be employed for imaging charges as small as a fraction of one elementary charge. The combination of these properties makes low-energy electrons an exciting tool for imaging charge transport in individual biomolecules. Here we demonstrate the imaging of individual deoxyribonucleic acid (DNA) molecules at the resolution of about 1 nm with simultaneous imaging of the charging of the DNA molecules that is of the order of less than one elementary charge per nanometer. The cross-correlation analysis performed on different sections of the DNA network reveals that the charge redistribution between the two regions is correlated. Thus, low-energy electron microscopy is capable to provide simultaneous imaging of macromolecular structure and its charge distribution which can be beneficial for imaging and constructing nano-bio-sensors.

cond-mat.mes-hall↗

arXiv2019

Lateral and axial resolution criteria in incoherent and coherent optics and holography, near- and far-field regimes

This work presents an overview of the spatial resolution criteria in classical optics, digital optics and holography. Although the classical Abbe and Rayleigh resolution criteria have been thoroughly discussed in the literature, there are still several issues which still need to be addressed, for example the axial resolution criterion for coherent and incoherent radiation, which is a crucial parameter of three-dimensional (3D) imaging, the resolution criteria in the Fresnel regime, and the lateral and axial resolution criteria in digital optics and holography. This work discusses these issues and provides a simple guide for which resolution criteria should be applied in each particular imaging scheme: coherent/incoherent, far- and near-field, lateral and axial resolution. Different resolution criteria such as two-point resolution and the resolution obtained from the image spectrum (diffraction pattern) are compared and demonstrated with simulated examples. Resolution criteria for spatial lateral and axial resolution are derived, and their application in imaging with coherent and incoherent (noncoherent) waves is considered. It is shown that for coherent light, the classical Abbe and Rayleigh resolution criteria do not provide an accurate estimation of the lateral and axial resolution. Lateral and axial resolution criteria based on an evaluation of the spectrum of the diffracted wave provide a more precise estimation of the resolution for coherent and incoherent light. It is also shown that resolution criteria derived in approximation of the far-field imaging regime can be applied for the near-field (Fresnel) regime.

physics.optics↗

arXiv2018

Moire structures in twisted bilayer graphene studied by transmission electron microscopy

We investigate imaging of moire structures in free-standing twisted bilayer graphene (TBG) carried out by transmission electron microscopy (TEM) in diffraction and in-line Gabor holography modes. Electron diffraction patterns of TBG acquired at typical TEM electron energies of 80 - 300 keV exhibit the diffraction peaks caused by diffraction on individual layers. However, diffraction peaks at the scattering angles related to the periodicity of the moire structure have not been observed in such diffraction patterns. We show that diffraction on moire structure can create intense diffraction peaks if the energy of the probing electrons is very low, in the range of a few tens of eV. Experimental diffraction patterns of TBG acquired with low-energy electrons of 236 eV exhibiting peaks attributed to the moire structure periodicity are shown. In holography mode, the intensity of the wave transmitted through the sample and measured in the far-field can be enhanced or decreased depending on the atomic arrangement, as for example AA or AB stacking. Thus, a decrease of intensity in the far-field must not necessarily be associated with some absorption inside the sample but can simply be a result of a particular atomic arrangement. We believe that our findings can be important for exploiting graphene as a support in electron imaging.

cond-mat.mes-hall↗

arXiv2018

Three-dimensional double helical DNA structure directly revealed from its X-ray fiber diffraction pattern by iterative phase retrieval

Coherent diffraction imaging (CDI) allows the retrieval of the structure of an isolated object, such as a macromolecule, from its diffraction pattern. CDI requires the fulfilment of two conditions: the imaging radiation must be coherent and the object must be isolated. We discuss that it is possible to directly retrieve the molecular structure from its diffraction pattern which was acquired neither with coherent radiation nor from an individual molecule, provided the molecule exhibits periodicity in one direction, as in the case of fiber diffraction. We demonstrate that by applying iterative phase retrieval methods to a fiber diffraction pattern, the repeating unit, that is, the molecule structure, can directly be reconstructed without any prior modeling. As an example, we recover the structure of the DNA double helix in three-dimensions from its two-dimensional X-ray fiber diffraction pattern, Photograph 51, acquired in the famous experiment by Raymond Gosling and Rosalind Franklin, at a resolution of 3.4 Angstrom.

physics.optics↗

arXiv2018

Convergent and divergent beam electron holography and reconstruction of adsorbates on free-standing two-dimensional crystals

Van der Waals heterostructures have been lately intensively studied because they offer a large variety of properties that can be controlled by selecting 2D materials and their sequence in the stack. The exact arrangement of the layers as well as the exact arrangement of the atoms within the layers, both are important for the properties of the resulting device. Recently it has been demonstrated that convergent beam electron diffraction (CBED) allows quantitative three-dimensional mapping of atomic positions in three-dimensional materials from a single CBED pattern. In this study we investigate CBED in more detail by simulating and performing various CBED regimes, with convergent and divergent wavefronts, on a somewhat simplified system: a 2D monolayer crystal. In CBED, each CBED spot is in fact an in-line hologram of the sample, where in-line holography is known to exhibit high intensity contrast in detection of weak phase objects that are not detectable in conventional in-focus imaging mode. Adsorbates exhibit strong intensity contrast in zero and higher order CBED spots, whereas lattice deformation such as strain or rippling cause noticeable intensity contrast only in the first and higher order CBED spots. The individual CBED spots can be reconstructed as typical in-line holograms, and the resolution of 2.13 A can be in principle achieved in the reconstructions. We provide simulated and experimental examples of CBED of a 2D monolayer crystal. The simulations show that individual CBED spots can be treated as in-line holograms and sample distributions such as adsorbates, can be reconstructed. Individual atoms can be reconstructed from a single CBED pattern provided the later exhibits high-order CBED spots. Examples of reconstructions obtained from experimental CBED patterns, at a resolution of 2.7 A, are shown.

cond-mat.mtrl-sci↗

arXiv2018

Iterative phase retrieval in coherent diffractive imaging: practical issues

In this work, issues in phase retrieval in the coherent diffractive imaging (CDI) technique, from discussion on parameters for setting up a CDI experiment to evaluation of the goodness of the final reconstruction, are discussed. The distribution of objects under study by CDI often cannot be cross-validated by another imaging technique. It is therefore important to make sure that the developed CDI procedure delivers an artifact-free object reconstruction. Critical issues that can lead to artifacts are presented and recipes on how to avoid them are provided.

physics.optics↗

arXiv2018

Local photo-mechanical stiffness revealed in gold nanoparticles supracrystals by ultrafast small-angle electron diffraction

We demonstrate that highly-ordered two-dimensional crystals of ligand-capped gold nanoparticles display a local photo-mechanical stiffness as high as that of solids such as graphite. In out-of equilibrium electron diffraction experiments, a strong temperature jump is induced in a thin film with a femtosecond laser pulse. The initial electronic excitation transfers energy to the underlying structural degrees of freedom, with a rate generally proportional to the stiffness of the material. With femtosecond small-angle electron diffraction, we observe the temporal evolution of the diffraction feature associated to the nearest-neighbor nanoparticle distance. The Debye-Waller decay for the octanethiol-capped nanoparticles supracrystal, in particular, is found to be unexpectedly fast, almost as fast as the stiffest solid known and observed by the same technique, i.e. graphite. Our observations unravel that local stiffness in a dense supramolecular assembly can be created by Van der Waals interactions up to a level comparable to crystalline systems characterized by covalent bonding.

cond-mat.mes-hall↗

arXiv2018

Algorithms and image formation in orbital tomography

Orbital tomography has recently been established as a technique to reconstruct molecular orbitals directly from photoemission data using iterative phase retrieval algorithms. In this work, we present a detailed description of steps for processing of the photoemission data followed by an improved iterative phase retrieval procedure and the interpretation of reconstructed two-dimensional orbital distributions. We address the issue of background subtraction by suggesting a signal restoration routine based on the maximization of mutual information algorithm and solve the problem of finding the geometrical center in the reconstruction by using a tight-centered object support in a two-step phase retrieval procedure. The proposed image processing and improved phase retrieval procedures are used to reconstruct the highest occupied molecular orbital of pentacene on Ag(110), using photoemission data only. The results of the reconstruction agree well with the density functional theory simulation, modified to comply with the experimental conditions. By comparison with photoelectron holography, we show that the reconstructed two-dimensional orbital distribution can be interpreted as a superposition of the in-focus orbital distribution evaluated at the z = 0 plane and out-of-focus distributions evaluated at other z = const planes. Three-dimensional molecular orbital distributions could thus be reconstructed directly from two-dimensional photoemission data, provided the axial resolution of the imaging system is high enough.

physics.chem-ph↗

arXiv2018

Convergent beam electron holography for analysis of van der Waals heterostructures

Van der Waals heterostructures, which explore the synergetic properties of two-dimensional (2D) materials when assembled into three-dimensional stacks, have already brought to life a number of exciting new phenomena and novel electronic devices. Still, the interaction between the layers in such assembly, possible surface reconstruction, intrinsic and extrinsic defects are very difficult to characterise by any method, because of the single-atomic nature of the crystals involved. Here we present a convergent beam electron holographic technique which allows imaging of the stacking order in such heterostructures. Based on the interference of electron waves scattered on different crystals in the stack, this approach allows one to reconstruct the relative rotation, stretching, out-of-plane corrugation of the layers with atomic precision. Being holographic in nature, our approach allows extraction of quantitative information about the three-dimensional structure of the typical defects from a single image covering thousands of square nanometres. Furthermore, qualitative information about the defects in the stack can be extracted from the convergent diffraction patterns even without reconstruction - simply by comparing the patterns in different diffraction spots. We expect that convergent beam electron holography will be widely used to study the properties of van der Waals heterostructures.

cond-mat.mes-hall↗

arXiv2017

Creating Airy beams employing a transmissive spatial light modulator

We present a detailed study of two novel methods for shaping the light optical wavefront by employing a transmissive spatial light modulator (SLM). Conventionally, optical Airy beams are created by employing SLMs in the so-called all phase mode. In the first method, a numerically simulated lens phase distribution is loaded directly onto the SLM, together with the cubic phase distribution. An Airy beam is generated at the focal plane of the numerical lens. We provide for the first time a quantitative properties of the formed Airy beam. We derive the formula for deflection of the intensity maximum of the so formed Airy beam, which is different to the quadratic deflection typical of Airy beams. We cross-validate the derived formula by both simulations and experiment. The second method is based on the fact that a system consisting of a transmissive SLM sandwiched between two polarisers can create a transmission function with negative values. This observation alone has the potential for various other wavefront modulations where the transmission function requires negative values. As an example for this method, we demonstrate that a wavefront can be modulated by passing the SLM system with transmission function with negative values by loading an Airy function distribution directly onto SLM. Since the Airy function is a real-valued function but also with negative values, an Airy beam can be generated by direct transfer of the Airy function distribution onto such an SLM system. In this way, an Airy beam is generated immediately behind the SLM. As both new methods do not employ a physical lens, the two setups are more compact than conventional setups for creating Airy beams. We compare the performance of the two novel methods and the properties of the created Airy beams.

physics.optics↗

arXiv2017

Resolution enhancement in in-line holography by numerical compensation of vibrations

Mechanical vibrations of components of the optical system is one of the sources of blurring of interference pattern in coherent imaging systems. The problem is especially important in holography where the resolution of the reconstructed objects depends on the effective size of the hologram, that is on the extent of the interference pattern, and on the contrast of the interference fringes. We discuss the mathematical relation between the vibrations, the hologram contrast and the reconstructed object. We show how vibrations can be post-filtered out from the hologram or from the reconstructed object assuming a Gaussian distribution of the vibrations. We also provide a numerical example of compensation for directional motion blur. We demonstrate our approach for light optical and electron holograms, acquired with both, plane- as well as spherical-waves. As a result of such hologram deblurring, the resolution of the reconstructed objects is enhanced by almost a factor of 2. We believe that our approach opens up a new venue of post-experimental resolution enhancement in in-line holography by adapting the rich database/catalogue of motion deblurring algorithms developed for photography and image restoration applications.

physics.optics↗

arXiv2017

Depth-resolved holographic reconstructions by three-dimensional deconvolution

Methods of three-dimensional deconvolution with a point-spread function as frequently employed in optical microscopy to reconstruct true three-dimensional distribution of objects are extended to holographic reconstructions. Two such schemes have been developed and are discussed: an instant deconvolution using the Wiener filter as well as an iterative deconvolution routine. The instant 3d-deconvolution can be applied to restore the positions of volume-spread objects such as small particles. The iterative deconvolution can be applied to restore the distribution of complex and extended objects. Simulated and experimental examples are presented and demonstrate artifact and noise free three-dimensional reconstructions from a single two-dimensional holographic record. Keywords: digital holography, volumetric deconvolution, three-dimensional volumetric deconvolution, particle tracking, holographic particle tracking, resolution, PSF

physics.optics↗

arXiv2017

Holographic time-resolved particle tracking by means of three-dimensional volumetric deconvolution

Holographic particle image velocimetry allows tracking particle trajectories in time and space by means of holography. However, the drawback of the technique is that in the three-dimensional particle distribution reconstructed from a hologram, the individual particles can hardly be resolved due to the superimposed out-of-focus signal from neighboring particles. We demonstrate here a three-dimensional volumetric deconvolution applied to the reconstructed wavefront which results in resolving all particles simultaneously in three-dimensions. Moreover, we apply the three-dimensional volumetric deconvolution to reconstructions of a time-dependent sequence of holograms of an ensemble of polystyrene spheres moving in water. From each hologram we simultaneously resolve all particles in the ensemble in three dimensions and from the sequence of holograms we obtain the time-resolved trajectories of individual polystyrene spheres.

physics.optics↗

arXiv2017

Imaging the potential distribution of individual charged impurities on graphene by low-energy electron holography

While imaging individual atoms can routinely be achieved in high resolution transmission electron microscopy, visualizing the potential distribution of individually charged adsorbates leading to a phase shift of the probing electron wave is still a challenging task. Low-energy electrons (30 - 250 eV) are sensitive to localized potential gradients. We employed low-energy electron holography to acquire in-line holograms of individual charged impurities on free-standing graphene. By applying an iterative phase retrieval reconstruction routine we recover the potential distribution of the localized charged impurities present on free-standing graphene.

cond-mat.mes-hall↗

arXiv2017

Spatial coherence of electron beams from field emitters and its effect on the resolution of imaged objects

Sub-nanometer and nanometer-sized tips provide high coherence electron sources. Conventionally, the effective source size is estimated from the extent of the experimental biprism interference pattern created on the detector by applying the van Cittert Zernike theorem. Previously reported experimental intensity distributions on the detector exhibit Gaussian distribution and our simulations show that this is an indication that such electron sources must be at least partially coherent. This, in turn means that strictly speaking the Van Cittert Zernike theorem cannot be applied, since it assumes an incoherent source. The approach of applying the van Cittert Zernike theorem is examined in more detail by performing simulations of interference patterns for the electron sources of different size and different coherence length, evaluating the effective source size from the extent of the simulated interference pattern and comparing the obtained result with the pre-defined value. The intensity distribution of the source is assumed to be Gaussian distributed, as it is observed in experiments. The visibility or the contrast in the simulated holograms is found to be always less than 1 which agrees well with previously reported experimental results and thus can be explained solely by the Gaussian intensity distribution of the source. The effective source size estimated from the extent of the interference pattern turns out to be of about 2-3 times larger than the pre-defined size, but it is approximately equal to the intrinsic resolution of the imaging system. A simple formula for estimating the intrinsic resolution, which could be useful when employing nano-tips in in-line Gabor holography or point-projection microscopy, is provided.

physics.ins-det↗

arXiv2017

Three-dimensional surface topography of graphene by divergent beam electron diffraction

There is only a handful of scanning techniques that can provide surface topography at nanometre resolution. At the same time, there are no methods that are capable of non-invasive imaging of the three-dimensional surface topography of a thin free-standing crystalline material. Here we propose a new technique - the divergent beam electron diffraction (DBED) and show that it can directly image the inhomogeneity in the atomic positions in a crystal. Such inhomogeneities are directly transformed into the intensity contrast in the first order diffraction spots of DBED patterns and the intensity contrast linearly depends on the wavelength of the employed probing electrons. Three-dimensional displacement of atoms as small as 1 angstrom can be detected when imaged with low-energy electrons (50 - 250 eV). The main advantage of DBED is that it allows visualisation of the three-dimensional surface topography and strain distribution at the nanometre scale in non-scanning mode, from a single shot diffraction experiment.

physics.ins-det↗

arXiv2017

Resolution enhancement in digital holography by self-extrapolation of holograms

It is generally believed that the resolution in digital holography is limited by the size of the captured holographic record. Here, we present a method to circumvent this limit by self-extrapolating experimental holograms beyond the area that is actually captured. This is done by first padding the surroundings of the hologram and then conducting an iterative reconstruction procedure. The wavefront beyond the experimentally detected area is thus retrieved and the hologram reconstruction shows enhanced resolution. To demonstrate the power of this concept, we apply it to simulated as well as experimental holograms.

physics.optics↗

arXiv2017

Imaging proteins at the truly single-molecule level

Imaging single proteins has been a long-standing ambition for advancing various fields in natural science, as for instance structural biology, biophysics and molecular nanotechnology. In particular, revealing the distinct conformations of an individual protein is of utmost importance. Here, we show the imaging of individual proteins and protein complexes by low-energy electron holography. Samples of individual proteins and protein complexes on ultraclean freestanding graphene were prepared by soft-landing electrospray ion beam deposition, which allows chemical- and conformational-specific selection and gentle deposition. Low-energy electrons do not induce radiation damage, which enables acquiring sub-nanometer resolution images of individual proteins (cytochrome C and bovine serum albumin) as well as of protein complexes (hemoglobin), which are not the result of an averaging process.

physics.bio-ph↗