Dose, exposure time, and resolution in Serial X-ray Crystallography

The resolution of X-ray diffraction microscopy is limited by the maximum dose that can be delivered prior to sample damage. In the proposed Serial Crystallography method, the damage problem is addressed by distributing the total dose over many identical hydrated macromolecules running continuously in a single-file train across a continuous X-ray beam, and resolution is then limited only by the available molecular and X-ray fluxes and molecular alignment. Orientation of the diffracting molecules is achieved by laser alignment. We evaluate the incident X-ray fluence (energy/area) required to obtain a given resolution from (1) an analytical model, giving the count rate at the maximum scattering angle for a model protein, (2) explicit simulation of diffraction patterns for a GroEL-GroES protein complex, and (3) the frequency cut off of the transfer function following iterative solution of the phase problem, and reconstruction of an electron density map in the projection approximation. These calculations include counting shot noise and multiple starts of the phasing algorithm. The results indicate counting time and the number of proteins needed within the beam at any instant for a given resolution and X-ray flux. We confirm an inverse fourth power dependence of exposure time on resolution, with important implications for all coherent X-ray imaging. We find that multiple single-file protein beams will be needed for sub-nanometer resolution on current third generation synchrotrons, but not on fourth generation designs, where reconstruction of secondary protein structure at a resolution of 0.7 nm should be possible with short exposures.Comment: 19 pages, 7 figures, 1 tabl

Viable thermionic emission from graphene-covered metals

Thermionic emission from monolayer graphene grown on representative transition metals, Ir and Ru, is characterized by low-energy electron microscopy (LEEM). Work functions were determined from the temperature dependence of the emission current and from the electron energy spectrum of emitted electrons. The high-temperature work function of the strongly interacting system graphene/Ru(0001) is sufficiently low, 3.3 \pm 0.1 eV, to have technological potential for large-area emitters that are spatially uniform, efficient, and chemically inert. The thermionic work functions of the less strongly interacting system graphene/Ir(111) are over 1 eV larger and vary substantially (0.4 eV) between graphene orientations rotated by 30{\deg}.Comment: Published in Applied Physics Letter

An assessment of the resolution limitation due to radiation-damage in x-ray diffraction microscopy

X-ray diffraction microscopy (XDM) is a new form of x-ray imaging that is being practiced at several third-generation synchrotron-radiation x-ray facilities. Although only five years have elapsed since the technique was first introduced, it has made rapid progress in demonstrating high-resolution threedimensional imaging and promises few-nm resolution with much larger samples than can be imaged in the transmission electron microscope. Both life- and materials-science applications of XDM are intended, and it is expected that the principal limitation to resolution will be radiation damage for life science and the coherent power of available x-ray sources for material science. In this paper we address the question of the role of radiation damage. We use a statistical analysis based on the so-called "dose fractionation theorem" of Hegerl and Hoppe to calculate the dose needed to make an image of a lifescience sample by XDM with a given resolution. We conclude that the needed dose scales with the inverse fourth power of the resolution and present experimental evidence to support this finding. To determine the maximum tolerable dose we have assembled a number of data taken from the literature plus some measurements of our own which cover ranges of resolution that are not well covered by reports in the literature. The tentative conclusion of this study is that XDM should be able to image frozen-hydrated protein samples at a resolution of about 10 nm with "Rose-criterion" image quality.Comment: 9 pages, 4 figure

Oxidation of graphene on metals

We use low-energy electron microscopy to investigate how graphene is removed from Ru(0001) and Ir(111) by reaction with oxygen. We find two mechanisms on Ru(0001). At short times, oxygen reacts with carbon monomers on the surrounding Ru surface, decreasing their concentration below the equilibrium value. This undersaturation causes a flux of carbon from graphene to the monomer gas. In this initial mechanism, graphene is etched at a rate that is given precisely by the same non-linear dependence on carbon monomer concentration that governs growth. Thus, during both growth and etching, carbon attaches and detaches to graphene as clusters of several carbon atoms. At later times, etching accelerates. We present evidence that this process involves intercalated oxygen, which destabilizes graphene. On Ir, this mechanism creates observable holes. It also occurs mostly quickly near wrinkles in the graphene islands, depends on the orientation of the graphene with respect to the Ir substrate, and, in contrast to the first mechanism, can increase the density of carbon monomers. We also observe that both layers of bilayer graphene islands on Ir etch together, not sequentially.Comment: 15 pages, 10 figures. Manuscript revised to improve discussion, following referee comments. Accepted for publication in Journal of Physical Chemistry C, Feb. 11, 201

Extraordinary epitaxial alignment of graphene islands on Au(111)

Pristine, single-crystalline graphene displays a unique collection of remarkable electronic properties that arise from its two-dimensional, honeycomb structure. Using in-situ low-energy electron microscopy, we show that when deposited on the (111) surface of Au carbon forms such a structure. The resulting monolayer, epitaxial film is formed by the coalescence of dendritic graphene islands that nucleate at a high density. Over 95% of these islands can be identically aligned with respect to each other and to the Au substrate. Remarkably, the dominant island orientation is not the better lattice-matched 30^{\circ} rotated orientation but instead one in which the graphene [01] and Au [011] in-plane directions are parallel. The epitaxial graphene film is only weakly coupled to the Au surface, which maintains its reconstruction under the slightly p-type doped graphene. The linear electronic dispersion characteristic of free-standing graphene is retained regardless of orientation. That a weakly interacting, non-lattice matched substrate is able to lock graphene into a particular orientation is surprising. This ability, however, makes Au(111) a promising substrate for the growth of single crystalline graphene films

Damped and thermal motion of large, laser-aligned molecules in droplet beams

We consider a monodispersed Rayleigh droplet beam of water droplets doped with proteins. An intense infrared laser is used to align these droplets. The arrangement has been proposed for electron and X-ray diffraction studies of proteins which are difficult to crystallize. This paper considers the effect of thermal fluctuations on the angular spread of alignment in thermal equilibrium, and relaxation phenomena, particularly the damping of oscillations excited as the molecules enter the field. The possibility of adiabatic alignment is also considered. We find that damping times in high pressure gas cell as used in X-ray diffraction experiments are short compared to the time taken for molecules to traverse the beam, and that a suitably shaped field might be used for electron diffraction experiments in vacuum to provide adiabatic alignment, thus obviating the need for a damping gas cell

Gas Dynamic Virtual Nozzle for Generation of Microscopic Droplet Streams

As shown by Ganan-Calvo and co-workers, a free liquid jet can be compressed in iameter through gas-dynamic forces exerted by a co-flowing gas, obviating the need for a solid nozzle to form a microscopic liquid jet and thereby alleviating the clogging problems that plague conventional droplet sources of small diameter. We describe in this paper a novel form of droplet beam source based on this principle. The source is miniature, robust, dependable, easily fabricated, and eminently suitable for delivery of microscopic liquid droplets, including hydrated biological samples, into vacuum for analysis using vacuum instrumentation. Monodisperse, single file droplet streams are generated by triggering the device with a piezoelectric actuator. The device is essentially immune to clogging