Imaging and Dynamics of Light Atoms and Molecules on Graphene

Observing the individual building blocks of matter is one of the primary goals of microscopy. The invention of the scanning tunneling microscope [1] revolutionized experimental surface science in that atomic-scale features on a solid-state surface could finally be readily imaged. However, scanning tunneling microscopy has limited applicability due to restrictions, for example, in sample conductivity, cleanliness, and data aquisition rate. An older microscopy technique, that of transmission electron microscopy (TEM) [2, 3] has benefited tremendously in recent years from subtle instrumentation advances, and individual heavy (high atomic number) atoms can now be detected by TEM [4 - 7] even when embedded within a semiconductor material [8, 9]. However, detecting an individual low atomic number atom, for example carbon or even hydrogen, is still extremely challenging, if not impossible, via conventional TEM due to the very low contrast of light elements [2, 3, 10 - 12]. Here we demonstrate a means to observe, by conventional transmision electron microscopy, even the smallest atoms and molecules: On a clean single-layer graphene membrane, adsorbates such as atomic hydrogen and carbon can be seen as if they were suspended in free space. We directly image such individual adatoms, along with carbon chains and vacancies, and investigate their dynamics in real time. These techniques open a way to reveal dynamics of more complex chemical reactions or identify the atomic-scale structure of unknown adsorbates. In addition, the study of atomic scale defects in graphene may provide insights for nanoelectronic applications of this interesting material.Comment: 9 pages manuscript and figures, 9 pages supplementary informatio

Three-dimensional structure determination from a single view

The ability to determine the structure of matter in three dimensions has profoundly advanced our understanding of nature. Traditionally, the most widely used schemes for 3D structure determination of an object are implemented by acquiring multiple measurements over various sample orientations, as in the case of crystallography and tomography (1,2), or by scanning a series of thin sections through the sample, as in confocal microscopy (3). Here we present a 3D imaging modality, termed ankylography (derived from the Greek words ankylos meaning 'curved' and graphein meaning 'writing'), which enables complete 3D structure determination from a single exposure using a monochromatic incident beam. We demonstrate that when the diffraction pattern of a finite object is sampled at a sufficiently fine scale on the Ewald sphere, the 3D structure of the object is determined by the 2D spherical pattern. We confirm the theoretical analysis by performing 3D numerical reconstructions of a sodium silicate glass structure at 2 Angstrom resolution and a single poliovirus at 2 - 3 nm resolution from 2D spherical diffraction patterns alone. Using diffraction data from a soft X-ray laser, we demonstrate that ankylography is experimentally feasible by obtaining a 3D image of a test object from a single 2D diffraction pattern. This approach of obtaining complete 3D structure information from a single view is anticipated to find broad applications in the physical and life sciences. As X-ray free electron lasers (X-FEL) and other coherent X-ray sources are under rapid development worldwide, ankylography potentially opens a door to determining the 3D structure of a biological specimen in a single pulse and allowing for time-resolved 3D structure determination of disordered materials.Comment: 30 page

3D diffractive imaging of nanoparticle ensembles using an X-ray laser

We report the 3D structure determination of gold nanoparticles (AuNPs) by X-ray single particle imaging (SPI). Around 10 million diffraction patterns from gold nanoparticles were measured in less than 100 hours of beam time, more than 100 times the amount of data in any single prior SPI experiment, using the new capabilities of the European X-ray free electron laser which allow measurements of 1500 frames per second. A classification and structural sorting method was developed to disentangle the heterogeneity of the particles and to obtain a resolution of better than 3 nm. With these new experimental and analytical developments, we have entered a new era for the SPI method and the path towards close-to-atomic resolution imaging of biomolecules is apparent

Ultrafast Light and Electrons: Imaging the Invisible

In this chapter, the evolutionary and revolutionary developments of microscopic imaging are overviewed with focus on ultrashort light and electrons pulses; for simplicity, we shall use the term “ultrafast” for both. From Alhazen’s camera obscura, to Hooke and van Leeuwenhoek’s optical micrography, and on to three- and four-dimensional (4D) electron microscopy, the developments over a millennium have transformed humans’ scope of visualization. The changes in the length and time scales involved are unimaginable, beginning with the visible shadows of candles at the centimeter and second scales, and ending with invisible atoms with space and time dimensions of sub-nanometer and femtosecond, respectively. With these advances it has become possible to determine the structures of matter and to observe their elementary dynamics as they fold and unfold in real time, providing the means for visualizing materials behavior and biological function, with the aim of understanding emergent phenomena in complex systems. Both light and light-generated electrons are now at the forefront of femtosecond and attosecond science and technology, and the scope of applications has reached beyond the nuclear motion as electron dynamics become accessible

Single-nanoparticle phase transitions visualized by four-dimensional electron microscopy

The advancement of techniques that can probe the behaviour of individual nanoscopic objects is of paramount importance in various disciplines, including photonics and electronics. As it provides images with a spatiotemporal resolution, four-dimensional electron microscopy, in principle, should enable the visualization of single-nanoparticle structural dynamics in real and reciprocal space. Here, we demonstrate the selectivity and sensitivity of the technique by visualizing the spin crossover dynamics of single, isolated metal–organic framework nanocrystals. By introducing a small aperture in the microscope, it was possible to follow the phase transition and the associated structural dynamics within a single particle. Its behaviour was observed to be distinct from that imaged by averaging over ensembles of heterogeneous nanoparticles. The approach reported here has potential applications in other nanosystems and those that undergo (bio)chemical transformations

Time-resolved single-crystal X-ray crystallography

In this chapter the development of time-resolved crystallography is traced from its beginnings more than 30 years ago. The importance of being able to “watch” chemical processes as they occur rather than just being limited to three-dimensional pictures of the reactant and final product is emphasised, and time-resolved crystallography provides the opportunity to bring the dimension of time into the crystallographic experiment. The technique has evolved in time with developments in technology: synchrotron radiation, cryoscopic techniques, tuneable lasers, increased computing power and vastly improved X-ray detectors. The shorter the lifetime of the species being studied, the more complex is the experiment. The chapter focusses on the results of solid-state reactions that are activated by light, since this process does not require the addition of a reagent to the crystalline material and the single-crystalline nature of the solid may be preserved. Because of this photoactivation, time-resolved crystallography is often described as “photocrystallography”. The initial photocrystallographic studies were carried out on molecular complexes that either underwent irreversible photoactivated processes where the conversion took hours or days. Structural snapshots were taken during the process. Materials that achieved a metastable state under photoactivation and the excited (metastable) state had a long enough lifetime for the data from the crystal to be collected and the structure solved. For systems with shorter lifetimes, the first time-resolved results were obtained for macromolecular structures, where pulsed lasers were used to pump up the short lifetime excited state species and their structures were probed by using synchronised X-ray pulses from a high-intensity source. Developments in molecular crystallography soon followed, initially with monochromatic X-ray radiation, and pump-probe techniques were used to establish the structures of photoactivated molecules with lifetimes in the micro- to millisecond range. For molecules with even shorter lifetimes in the sub-microsecond range, Laue diffraction methods (rather than using monochromatic radiation) were employed to speed up the data collections and reduce crystal damage. Future developments in time-resolved crystallography are likely to involve the use of XFELs to complete “single-shot” time-resolved diffraction studies that are already proving successful in the macromolecular crystallographic field.</p

Ptychography

Ptychography is a computational imaging technique. A detector records an extensive data set consisting of many inference patterns obtained as an object is displaced to various positions relative to an illumination field. A computer algorithm of some type is then used to invert these data into an image. It has three key advantages: it does not depend upon a good-quality lens, or indeed on using any lens at all; it can obtain the image wave in phase as well as in intensity; and it can self-calibrate in the sense that errors that arise in the experimental set up can be accounted for and their effects removed. Its transfer function is in theory perfect, with resolution being wavelength limited. Although the main concepts of ptychography were developed many years ago, it has only recently (over the last 10 years) become widely adopted. This chapter surveys visible light, x-ray, electron, and EUV ptychography as applied to microscopic imaging. It describes the principal experimental arrangements used at these various wavelengths. It reviews the most common inversion algorithms that are nowadays employed, giving examples of meta code to implement these. It describes, for those new to the field, how to avoid the most common pitfalls in obtaining good quality reconstructions. It also discusses more advanced techniques such as modal decomposition and strategies to cope with three-dimensional () multiple scattering