Scanning ultrafast electron microscopy

Progress has been made in the development of four-dimensional ultrafast electron microscopy, which enables space-time imaging of structural dynamics in the condensed phase. In ultrafast electron microscopy, the electrons are accelerated, typically to 200 keV, and the microscope operates in the transmission mode. Here, we report the development of scanning ultrafast electron microscopy using a field-emission-source configuration. Scanning of pulses is made in the single-electron mode, for which the pulse contains at most one or a few electrons, thus achieving imaging without the space-charge effect between electrons, and still in ten(s) of seconds. For imaging, the secondary electrons from surface structures are detected, as demonstrated here for material surfaces and biological specimens. By recording backscattered electrons, diffraction patterns from single crystals were also obtained. Scanning pulsed-electron microscopy with the acquired spatiotemporal resolutions, and its efficient heat-dissipation feature, is now poised to provide in situ 4D imaging and with environmental capability.     

From the Cover: Goniometer-based femtosecond crystallography with X-ray free electron lasers

The emerging method of femtosecond crystallography (FX) may extend the diffraction resolution accessible from small radiation-sensitive crystals and provides a means to determine catalytically accurate structures of acutely radiation-sensitive metalloenzymes. Automated goniometer-based instrumentation developed for use at the Linac Coherent Light Source enabled efficient and flexible FX experiments to be performed on a variety of sample types. In the case of rod-shaped Cpl hydrogenase crystals, only five crystals and about 30 min of beam time were used to obtain the 125 still diffraction patterns used to produce a 1.6-Å resolution electron density map. For smaller crystals, high-density grids were used to increase sample throughput; 930 myoglobin crystals mounted at random orientation inside 32 grids were exposed, demonstrating the utility of this approach. Screening results from cryocooled crystals of β₂-adrenoreceptor and an RNA polymerase II complex indicate the potential to extend the diffraction resolution obtainable from very radiation-sensitive samples beyond that possible with undulator-based synchrotron sources.Using extremely bright, short-timescale X-ray pulses produced by X-ray free-electron lasers (XFELs), femtosecond crystallography (FX) is an emerging method that expands the structural information accessible from very small or very radiation-sensitive macromolecular crystals. Central to this method is the “diffraction before destruction” (1) process in which a still diffraction image is produced by a single X-ray pulse before significant radiation-induced electronic and atomic rearrangements occur within the crystal (1–3). At the Linac Coherent Light Source (LCLS) at SLAC, a single ∼50-fs–long X-ray pulse can expose a crystal to as many X-ray photons as a typical synchrotron beam line produces in about a second. Exposing small crystals to these intense ultrashort pulses circumvents the dose limitations of conventional X-ray diffraction experiments (4) and may produce useful data to resolutions beyond what is achievable at synchrotrons (5). This innovation provides a pathway to obtain atomic information from proteins that only form micrometer- to nanometer-sized crystals, such as many membrane proteins and large multiprotein complexes. Moreover, XFELs enable “diffraction before reduction” data collection to address another major challenge in structural enzymology by providing a means to determine catalytically accurate structures of acutely radiation-sensitive metalloenzyme active sites (6), such as high-valency reaction intermediates that may be significantly photoreduced during a single X-ray exposure at a synchrotron, even at very small doses (7–11). Furthermore, the use of short (tens of femtoseconds) X-ray pulses further complements the structural characterization of biochemical reaction processes by providing access to a time domain two to three orders of magnitude faster (12, 13) than currently accessible using synchrotrons.A single X-ray pulse from the LCLS damages the illuminated sample volume and also some of the sample in the immediate vicinity, requiring the combination of measurements from discrete volumes or units of crystalline material to obtain a complete dataset (14). The first FX experiments were carried out in vacuum at the LCLS using a gas dynamic virtual nozzle (GDVN) liquid injector (15), which delivered crystals of submicron to a few microns in size, suspended in carrier solution to a series of X-ray pulses produced at up to a 120-Hz repetition rate. These pioneering experiments demonstrated the utility of serial femtosecond crystallography (SFX) and the use of crystals of less than 5 μm in size, often termed “nanocrystals” (NCs), for macromolecular structure determination to high resolution (16, 17). As NCs may be a ubiquitous but generally overlooked outcome of commercial crystallization screens that fail to produce larger crystals (18), FX may open up many systems to crystallographic analysis. However, to develop FX into a generally applicable method, a number of challenges in the areas of sample preparation, data collection, and data processing must be overcome.Obtaining a sufficient supply of crystals in an appropriate carrier solution is a first hurdle to conducting a SFX experiment. In addition to the GDVN (2, 3, 14, 16, 17, 19, 20), other injectors such as a nanoflow electrospinning injector (21) and a lipidic cubic phase (LCP) injector (22), have been developed that have a reduced flow rate and lower sample consumption. However, because injectors deliver a continuous stream of solution containing a random distribution of crystals, and the X-ray pulses are extremely short, often only a small percentage of pulses hit a crystal and produce a useful diffraction pattern. Carrying out these experiments at room temperature avoids the difficulties associated with cryoprotection, and datasets obtained at ambient temperatures can provide insight on the functional motions of protein molecules (23). However, there are different and often more complex optimization steps associated with specific injector technologies. Solutions containing a mixture of crystal sizes may require filtering to avoid clogging in the injector nozzle, and delicate crystals may be damaged from the pressures and shear forces of the delivery process itself (24). For experiments conducted in vacuo, stream formation may be disrupted by solution bubbling, drying, or freezing as it exits the injector and enters the vacuum chamber. Drop-on-demand methods that deliver single drops containing crystals to individual X-ray pulses have the potential to significantly reduce sample consumption are in development, such as acoustic and micropiezo activated technologies, but implementation has been complicated by a variety of factors, including difficulties imposed by viscous solutions and unpredictable trajectories of drops that contain crystals of varied shapes and sizes.Here, we describe an alternative strategy for FX experiments that leverages the well-established benefits of the highly automated goniometer-based setups used at state-of-the-art microfocus synchrotron beam lines, and expands these technologies to take full advantage of the unique capabilities of XFEL sources. Key to this approach is the coupling of highly automated instrumentation with specialized sample containers and customized software for efficient data collection with minimal sample consumption. High-density sample containers, such as microfluidic chips or microcrystal traps (25) for room temperature studies or grids for experiments at cryogenic temperatures, hold samples in known locations. These sample holders enable very rapid and precise positioning of crystals into the X-ray interaction region for consistent production of diffraction patterns. To optimize data completeness and resolution, data may be collected using a range of crystal sizes with a variety of X-ray beam sizes, and different regions of larger crystals may be exposed in different orientations. When small crystals align with the sample holder in a preferred orientation, exposing each crystal at varied angles to the holder surface may take advantage of this effect to enhance completeness. When the X-ray pulse mean diameter is greater than about 8 μm or is highly attenuated, the protein crystal may remain intact after exposure to the X-ray pulse and still diffract, but usually to a lower resolution as a result of radiation damage. In these cases, it is possible to rotate the crystal and collect additional diffraction patterns to use as an aid in indexing and scaling the partially recorded reflections of the initial still diffraction pattern.     

Single-electron pulses for ultrafast diffraction

Visualization of atomic-scale structural motion by ultrafast electron diffraction and microscopy requires electron packets of shortest duration and highest coherence. We report on the generation and application of single-electron pulses for this purpose. Photoelectric emission from metal surfaces is studied with tunable ultraviolet pulses in the femtosecond regime. The bandwidth, efficiency, coherence, and electron pulse duration are investigated in dependence on excitation wavelength, intensity, and laser bandwidth. At photon energies close to the cathode's work function, the electron pulse duration shortens significantly and approaches a threshold that is determined by interplay of the optical pulse width and the acceleration field. An optimized choice of laser wavelength and bandwidth results in sub-100-fs electron pulses. We demonstrate single-electron diffraction from polycrystalline diamond films and reveal the favorable influences of matched photon energies on the coherence volume of single-electron wave packets. We discuss the consequences of our findings for the physics of the photoelectric effect and for applications of single-electron pulses in ultrafast 4D imaging of structural dynamics.     

Breaking resolution limits in ultrafast electron diffraction and microscopy

Ultrafast electron microscopy and diffraction are powerful techniques for the study of the time-resolved structures of molecules, materials, and biological systems. Central to these approaches is the use of ultrafast coherent electron packets. The electron pulses typically have an energy of 30 keV for diffraction and 100-200 keV for microscopy, corresponding to speeds of 33-70% of the speed of light. Although the spatial resolution can reach the atomic scale, the temporal resolution is limited by the pulse width and by the difference in group velocities of electrons and the light used to initiate the dynamical change. In this contribution, we introduce the concept of tilted optical pulses into diffraction and imaging techniques and demonstrate the methodology experimentally. These advances allow us to reach limits of time resolution down to regimes of a few femtoseconds and, possibly, attoseconds. With tilted pulses, every part of the sample is excited at precisely the same time as when the electrons arrive at the specimen. Here, this approach is demonstrated for the most unfavorable case of ultrafast crystallography. We also present a method for measuring the duration of electron packets by autocorrelating electron pulses in free space and without streaking, and we discuss the potential of tilting the electron pulses themselves for applications in domains involving nuclear and electron motions.     

Attosecond electron pulses for 4D diffraction and microscopy

In this contribution, we consider the advancement of ultrafast electron diffraction and microscopy to cover the attosecond time domain. The concept is centered on the compression of femtosecond electron packets to trains of 15-attosecond pulses by the use of the ponderomotive force in synthesized gratings of optical fields. Such attosecond electron pulses are significantly shorter than those achievable with extreme UV light sources near 25 nm ( approximately 50 eV) and have the potential for applications in the visualization of ultrafast electron dynamics, especially of atomic structures, clusters of atoms, and some materials.     

Ultrafast large-amplitude relocation of electronic charge in ionic crystals

The interplay of vibrational motion and electronic charge relocation in an ionic hydrogen-bonded crystal is mapped by X-ray powder diffraction with a 100 fs time resolution. Photoexcitation of the prototype material KH₂PO₄ induces coherent low-frequency motions of the PO₄ tetrahedra in the electronically excited state of the crystal while the average atomic positions remain unchanged. Time-dependent maps of electron density derived from the diffraction data demonstrate an oscillatory relocation of electronic charge with a spatial amplitude two orders of magnitude larger than the underlying vibrational lattice motions. Coherent longitudinal optical and tranverse optical phonon motions that dephase on a time scale of several picoseconds, drive the charge relocation, similar to a soft (transverse optical) mode driven phase transition between the ferro- and paraelectric phase of KH₂PO₄.     

Ultrafast electron crystallography: transient structures of molecules, surfaces, and phase transitions

The static structure of macromolecular assemblies can be mapped out with atomic-scale resolution by using electron diffraction and microscopy of crystals. For transient nonequilibrium structures, which are critical to the understanding of dynamics and mechanisms, both spatial and temporal resolutions are required; the shortest scales of length (0.1-1 nm) and time (10(-13) to 10(-12) s) represent the quantum limit, the nonstatistical regime of rates. Here, we report the development of ultrafast electron crystallography for direct determination of structures with submonolayer sensitivity. In these experiments, we use crystalline silicon as a template for different adsorbates: hydrogen, chlorine, and trifluoroiodomethane. We observe the coherent restructuring of the surface layers with subangstrom displacement of atoms after the ultrafast heat impulse. This nonequilibrium dynamics, which is monitored in steps of 2 ps (total change 相似文献   

Applications of synchrotron radiation to protein crystallography: preliminary results.

X-ray diffraction photographs of protein single crystals have been obtained using synchrotron radiation produced by an electron-positron storage ring. The diffracted intensities observed with this unconventional source are a factor of at least 60 greater than those obtained with a sealed x-ray tube using the same crystal and instrumental parameters. Diffraction data have been collected by the precession method to higher resolution and using smaller protein crystals than would have been possible with a conventional source. The crystal decay rate in the synchrotron beam for several proteins appears to be substantially less than that observed with Ni-filtered Cu radiation. The tunable nature of the source (which allows selective optimization of anomalous contributions to the scattering factors) and the low angular divergence of the beam make the source very useful for single crystal protein diffraction studies.     

An approach to three-dimensional structures of biomolecules by using single-molecule diffraction images

We describe an approach to the high-resolution three-dimensional structural determination of macromolecules that utilizes ultrashort, intense x-ray pulses to record diffraction data in combination with direct phase retrieval by the oversampling technique. It is shown that a simulated molecular diffraction pattern at 2.5-A resolution accumulated from multiple copies of single rubisco biomolecules, each generated by a femtosecond-level x-ray free electron laser pulse, can be successfully phased and transformed into an accurate electron density map comparable to that obtained by more conventional methods. The phase problem is solved by using an iterative algorithm with a random phase set as an initial input. The convergence speed of the algorithm is reasonably fast, typically around a few hundred iterations. This approach and phasing method do not require any ab initio information about the molecule, do not require an extended ordered lattice array, and can tolerate high noise and some missing intensity data at the center of the diffraction pattern. With the prospects of the x-ray free electron lasers, this approach could provide a major new opportunity for the high-resolution three-dimensional structure determination of single biomolecules.     

4D multiple-cathode ultrafast electron microscopy

Four-dimensional multiple-cathode ultrafast electron microscopy is developed to enable the capture of multiple images at ultrashort time intervals for a single microscopic dynamic process. The dynamic process is initiated in the specimen by one femtosecond light pulse and probed by multiple packets of electrons generated by one UV laser pulse impinging on multiple, spatially distinct, cathode surfaces. Each packet is distinctly recorded, with timing and detector location controlled by the cathode configuration. In the first demonstration, two packets of electrons on each image frame (of the CCD) probe different times, separated by 19 picoseconds, in the evolution of the diffraction of a gold film following femtosecond heating. Future elaborations of this concept to extend its capabilities and expand the range of applications of 4D ultrafast electron microscopy are discussed. The proof-of-principle demonstration reported here provides a path toward the imaging of irreversible ultrafast phenomena of materials, and opens the door to studies involving the single-frame capture of ultrafast dynamics using single-pump/multiple-probe, embedded stroboscopic imaging.In 4D ultrafast electron microscopy (UEM), ultrafast light pulses generate electron packets by photoemission at the cathode of an electron microscope, and these are used to probe a dynamic process initiated by heating or exciting the microscopic specimen with a second, synchronized ultrafast light pulse (1, 2). In conventional implementations, each pump pulse on the specimen is accompanied by one suitably delayed laser pulse on the cathode to generate one packet of electrons probing a single time point in the evolution of the specimen. A record of the full course of temporal evolution of the specimen is then constructed by repeating the experiment multiple times with variation of the delay time between the two light pulses, reading out a separate CCD image for each delay time. Thus, information about different time points in the dynamic response of the specimen is obtained from different excitation events. This implementation is ideally suited for a specimen that undergoes irreversible but sufficiently well-defined dynamics to allow a new specimen area to be used for each time point (Fig. 1A), or for a specimen that recovers fully to allow repeated identical excitations of the same area (Fig. 1B); see also Methodology. The applications of these two approaches are numerous, as highlighted in a recent review account of the work (3).Open in a separate windowFig. 1.Variant implementations of UEM. (A) Single-pulse UEM, which enables single-shot imaging of homogeneous specimens. (B) Stroboscopic UEM. (D) Multiple-cathode UEM. For comparison, we include, in C, the single-cathode, deflection method. See text for details.For the study of completely nonrepetitive dynamics, for example, a stochastic process in a heterogeneous sample that does not return to its initial configuration, a series of snapshots following a single excitation event can provide the only direct and detailed view of the evolution. Observing the effects of a single excitation pulse with video-mode imaging can currently reach millisecond-scale time resolution, far short of the time scale for many phenomena of interest in nanoscale materials science, chemistry, and physics. Nanosecond resolution has been reached (4) by combining one excitation pulse with a train of light pulses on a single cathode, with deflection of the imaging electrons after passing the specimen plane to direct each successive pulse to a new region of the detector (Fig. 1C). This nanosecond method has been successfully used with a high-speed electrostatic deflector array to obtain time sequences of irreversible and stochastic processes (5, 6).Here we demonstrate a technique that removes any limit on time resolution imposed by image deflection and in a single frame enables the capture of ultrafast phenomena. With this approach, it is possible to probe and distinctly record multiple time points in a dynamic process following a single initiation pulse. The probing electron packets are all generated by a single light pulse that impinges on multiple, spatially distinct, cathode surfaces (Fig. 1D). Time separations between packets in the electron-pulse train are adjusted by the cathode spatial and electrostatic configuration. In the present application, two electron packets, generated from two source locations at the same potential and separated in time by 19 picoseconds (ps), are recorded on each CCD frame after undergoing diffraction in a gold film following femtosecond heating. The packets originate from different cathode locations, pass through the same area of the specimen, and are recorded at distinct locations on the detector, thereby encoding two different time points in the evolution of the specimen. The results obtained provide the basis for exploration of expanded application of the multiple-cathode concept.     

Observation of femtosecond X-ray interactions with matter using an X-ray–X-ray pump–probe scheme

Resolution in the X-ray structure determination of noncrystalline samples has been limited to several tens of nanometers, because deep X-ray irradiation required for enhanced resolution causes radiation damage to samples. However, theoretical studies predict that the femtosecond (fs) durations of X-ray free-electron laser (XFEL) pulses make it possible to record scattering signals before the initiation of X-ray damage processes; thus, an ultraintense X-ray beam can be used beyond the conventional limit of radiation dose. Here, we verify this scenario by directly observing femtosecond X-ray damage processes in diamond irradiated with extraordinarily intense (∼10¹⁹ W/cm²) XFEL pulses. An X-ray pump–probe diffraction scheme was developed in this study; tightly focused double–5-fs XFEL pulses with time separations ranging from sub-fs to 80 fs were used to excite (i.e., pump) the diamond and characterize (i.e., probe) the temporal changes of the crystalline structures through Bragg reflection. It was found that the pump and probe diffraction intensities remain almost constant for shorter time separations of the double pulse, whereas the probe diffraction intensities decreased after 20 fs following pump pulse irradiation due to the X-ray–induced atomic displacement. This result indicates that sub-10-fs XFEL pulses enable conductions of damageless structural determinations and supports the validity of the theoretical predictions of ultraintense X-ray–matter interactions. The X-ray pump–probe scheme demonstrated here would be effective for understanding ultraintense X-ray–matter interactions, which will greatly stimulate advanced XFEL applications, such as atomic structure determination of a single molecule and generation of exotic matters with high energy densities.Since W. C. Röntgen discovered X-rays emitted from vacuum tube equipment in 1895, scientists have continuously endeavored to develop brighter X-ray sources throughout the 20th century. One of the most remarkable breakthroughs was the emergence of synchrotron light sources, which were much more brilliant than the early lab-based X-ray sources. Such dramatic increase in X-ray brilliance provided a pathway to obtain high-quality X-ray scattering data. This, in turn, enabled one to solve the structures of complex systems such as proteins, functional units of living organisms, and viruses. However, the increase in the brilliance is also accompanied by a severe problem of X-ray radiation damage to the samples being examined (1). X-rays ionize atoms and generate highly activated radicals that break chemical bonds and cause changes in the structures of the samples. To achieve structure determination precisely, a sufficient scattering signal should be recorded before the samples are severely damaged. Radiation damage was considered to be an intrinsic problem associated with X-ray scattering experiments, which imposed a fundamental limit on the resolution in X-ray structure determination (2).The recent advent of X-ray free-electron lasers (XFELs) (3–5), which emit ultraintense X-ray pulses with durations of several femtoseconds, may totally avoid the problem of radiation damage. The irradiation of intense XFEL pulses generates highly ionized atoms, and the strong Coulomb repulsive force leads to evaporation of the samples. Meanwhile, it has been predicted theoretically (6) that atoms do not change their positions before the termination of the femtosecond X-ray pulse owing to inertia, thus enabling the use of X-ray radiations beyond the conventional X-ray dose limit. This innovative concept, called a “diffraction-before-destruction” scheme (6, 7), has paved a clear way to high-resolution structure determinations of weak scattering objects, including nanometer-sized protein crystals (8), noncrystalline biological particles (9), and damage-sensitive protein crystals (10).Despite the potential impact of XFELs, detailed understanding of the ultrafast XFEL damage processes has been missing. As a pioneering work, Barty et al. (11) measured the diffraction intensities of protein nanocrystals by changing the XFEL pulse durations from 70 to 300 fs at intensities of ∼10¹⁷ W/cm². They found that the diffraction intensities greatly decrease for longer durations, clearly indicating sign of structural damage, i.e., X-ray–induced atomic displacements within the XFEL pulse durations. For further understanding of ultraintense X-ray interactions with matter, we need to directly measure the temporal changes of the structural damage. In particular, measuring the ignition time of the atomic displacements is crucial for realizing advanced applications with greatly intense XFELs. Although improving our knowledge of the X-ray damage processes is essential for all aspects of XFEL science, the experimental verifications have been missing because of the extreme difficulty in observation with ultrahigh resolutions in space (ångstrom) and time (femtosecond).As a new approach to investigate the femtosecond X-ray damage processes, we here propose an X-ray–X-ray pump–probe experiment using double X-ray pulses; a pump X-ray pulse excites a sample and a probe X-ray pulse with a well-controlled time delay characterizes the change in the sample. In this approach, it is highly useful to exploit two-color double pulses with tunable temporal separations (12–15), which have been developed at SPring-8 Angstrom Compact free-electron LAser (SACLA) (4) and Linac Coherent Light Source (3). In this article, we measured the X-ray damage processes of diamond by using an X-ray–X-ray pump–probe diffraction experiment at SACLA. As the carbon–carbon bond is one of the most fundamental bonds in biomolecules, our results should provide a benchmark for XFEL-induced damage to practical samples.     

Femtosecond time resolution in x-ray diffraction experiments

This paper presents the theoretical background for a synthesis of femtosecond spectroscopy and x-ray diffraction. When a diffraction quality crystal with 0.1–0.3 mm overall dimensions is photoactivated by a femtosecond laser pulse (physical length = 0.3 μm), the evolution of molecules at separated points in the crystal will not be simultaneous because a finite time is required for the laser pulse to propagate through the body of the crystal. Utilizing this lack of global crystal synchronization, topographic x-ray diffraction may enable femtosecond temporal resolution to be achieved from reflection profiles in the diffraction pattern with x-ray exposures of picosecond or longer duration. Such x-ray pulses are currently available, and could be used to study femtosecond reaction dynamics at atomic resolution on crystals of both small- and macromolecules. A general treatment of excitation and diffraction geometries in relation to spatial and temporal resolution is presented.     

Crystal engineering rescues a solution organic synthesis in a cocrystallization that confirms the configuration of a molecular ladder

Treatment of an achiral molecular ladder of C(2h) symmetry composed of five edge-sharing cyclobutane rings, or a [5]-ladderane, with acid results in cis- to trans-isomerization of end pyridyl groups. Solution NMR spectroscopy and quantum chemical calculations support the isomerization to generate two diastereomers. The NMR data, however, could not lead to unambiguous configurational assignments of the two isomers. Single-crystal X-ray diffraction was employed to determine each configuration. One isomer readily crystallized as a pure form and X-ray diffraction revealed the molecule as being achiral based on C(i) symmetry. The second isomer resisted crystallization under a variety of conditions. Consequently, a strategy based on a cocrystallization was developed to generate single crystals of the second isomer. Cocrystallization of the isomer with a carboxylic acid readily afforded single crystals that confirmed a chiral ladderane based on C(2) symmetry. The chiral ladderane and acid self-assembled to generate a five-component hydrogen-bonded complex that packs to form large solvent-filled homochiral channels of nanometer-scale dimensions. Whereas cocrystallizations are frequently applied to structure determinations of proteins, our study represents the first application of a cocrystallization to confirm the relative configuration of a small-molecule diastereomer generated in a solution-phase organic synthesis.     

Temporal lenses for attosecond and femtosecond electron pulses

Here, we describe the “temporal lens” concept that can be used for the focus and magnification of ultrashort electron packets in the time domain. The temporal lenses are created by appropriately synthesizing optical pulses that interact with electrons through the ponderomotive force. With such an arrangement, a temporal lens equation with a form identical to that of conventional light optics is derived. The analog of ray diagrams, but for electrons, are constructed to help the visualization of the process of compressing electron packets. It is shown that such temporal lenses not only compensate for electron pulse broadening due to velocity dispersion but also allow compression of the packets to durations much shorter than their initial widths. With these capabilities, ultrafast electron diffraction and microscopy can be extended to new domains,and, just as importantly, electron pulses can be delivered directly on an ultrafast techniques target specimen.     

Acid-induced structural changes in human rhinovirus 14: possible role in uncoating.

X-ray diffraction data were collected from human rhinovirus 14 crystals a few minutes after exposure to acid vapor and prior to excessive crystalline disorder. Conformational changes occurred (i) in the GH loop of viral protein (VP) 1, (ii) at the ion binding site on the outer surface of the pentamer center, and (iii) in VP3 and VP4 on the virion's interior in the vicinity of the fivefold axis. Amino acid substitutions in mutants resistant to low pH, or to drugs that inhibit uncoating, were concentrated in the vicinity of the GH loop. It is proposed that the acid-induced changes reflect processes that trigger uncoating.     

Four-dimensional ultrafast electron microscopy

Electron microscopy is arguably the most powerful tool for spatial imaging of structures. As such, 2D and 3D microscopies provide static structures with subnanometer and increasingly with ångstrom-scale spatial resolution. Here we report the development of 4D ultrafast electron microscopy, whose capability imparts another dimension to imaging in general and to dynamics in particular. We demonstrate its versatility by recording images and diffraction patterns of crystalline and amorphous materials and images of biological cells. The electron packets, which were generated with femtosecond laser pulses, have a de Broglie wavelength of 0.0335 Å at 120 keV and have as low as one electron per pulse. With such few particles, doses of few electrons per square ångstrom, and ultrafast temporal duration, the long sought after but hitherto unrealized quest for ultrafast electron microscopy has been realized. Ultrafast electron microscopy should have an impact on all areas of microscopy, including biological imaging.     

Algorithmic framework for X-ray nanocrystallographic reconstruction in the presence of the indexing ambiguity

X-ray nanocrystallography allows the structure of a macromolecule to be determined from a large ensemble of nanocrystals. However, several parameters, including crystal sizes, orientations, and incident photon flux densities, are initially unknown and images are highly corrupted with noise. Autoindexing techniques, commonly used in conventional crystallography, can determine orientations using Bragg peak patterns, but only up to crystal lattice symmetry. This limitation results in an ambiguity in the orientations, known as the indexing ambiguity, when the diffraction pattern displays less symmetry than the lattice and leads to data that appear twinned if left unresolved. Furthermore, missing phase information must be recovered to determine the imaged object’s structure. We present an algorithmic framework to determine crystal size, incident photon flux density, and orientation in the presence of the indexing ambiguity. We show that phase information can be computed from nanocrystallographic diffraction using an iterative phasing algorithm, without extra experimental requirements, atomicity assumptions, or knowledge of similar structures required by current phasing methods. The feasibility of this approach is tested on simulated data with parameters and noise levels common in current experiments.Although conventional X-ray crystallography has been used extensively to determine atomic structure, it is limited to objects that can be formed into large crystal samples . An appealing alternative, made possible by recent advances in light source technology, is X-ray nanocrystallography, which is able to image structures resistant to large crystallization, such as membrane proteins, by substituting a large ensemble of easier to build nanocrystals, typically , often delivered to the beam via a liquid jet (1–6) (Fig. 1). However, the beam power required to retrieve sufficient information destroys the crystal, hence ultrafast pulses (≤70 fs) are required to collect data before damage effects alter the signal. Using nanocrystals introduces several challenges. Due to the small crystal size, Bragg peaks are smeared out, and there is noticeable signal between peaks. Typically, only partial peak reflections are measured, resulting in reduced intensities. Variations in crystal size and incident photon flux density, unknown orientations, shot noise, and background signal from the liquid and detector add additional uncertainty to the data.Open in a separate windowFig. 1.Liquid jet (blue) delivers nanocrystal samples to the X-ray beam (red). Wide- and small-angle diffraction data are collected using front and rear detectors.If crystal orientations were known, noise and variation in the peak measurements could be averaged out, and the data could be inverted to retrieve the object’s electron density. Although autoindexing techniques can be used to determine crystal orientation up to lattice symmetry from the location of a sufficient number of Bragg peaks, they typically face difficulties in the presence of partial and non-Bragg reflections common in nanocrystal diffraction images. Furthermore, these techniques only narrow down orientation to a list of possibilities when the diffraction pattern has less symmetry than the lattice, leading to an ambiguity in the image orientation, known as the indexing ambiguity. Current methods of processing the diffraction data are largely based on averaging out the data variance over several images (1–8). However, if the data are processed without resolving the indexing ambiguity then they will appear to be perfectly twinned, i.e., averaged over multiple orientations. Although there has been some success in determining structure from perfectly twinned data, reconstruction is often infeasible without a good initial atomic model of the structure.We present an algorithmic framework for X-ray nanocrystallographic reconstruction which is based on directly reducing data variance and resolving the indexing ambiguity. First, we design an autoindexing technique that uses both Bragg and non-Bragg data to compute precise orientations, up to lattice symmetry. Crystal sizes are then determined by performing a Fourier analysis around Bragg peak neighborhoods from a finely sampled low-angle image, such as from a rear detector (Fig. 1). Next, we model structure factor magnitudes for each reciprocal lattice point with a multimodal Gaussian distribution, using a multistage expectation maximization algorithm which simultaneously scales and models the data. These multimodal models are used to build a weighted graph which models the structure factor magnitude concurrency. We formulate the solution to the indexing ambiguity problem as finding the maximum edge weight clique in this graph, which can be solved efficiently via a greedy approach. Finally, we demonstrate the feasibility of solving the phase problem using iterative phase retrieval. Whereas several of the presented methods rely on the use of nanocrystals, we note that the scaling–multimodal analysis and indexing ambiguity resolution steps can also be applied to larger crystals .     

Direct role of structural dynamics in electron-lattice coupling of superconducting cuprates

The mechanism of electron pairing in high-temperature superconductors is still the subject of intense debate. Here, we provide direct evidence of the role of structural dynamics, with selective atomic motions (buckling of copper–oxygen planes), in the anisotropic electron-lattice coupling. The transient structures were determined using time-resolved electron diffraction, following carrier excitation with polarized femtosecond heating pulses, and examined for different dopings and temperatures. The deformation amplitude reaches 0.5% of the c axis value of 30 Å when the light polarization is in the direction of the copper–oxygen bond, but its decay slows down at 45°. These findings suggest a selective dynamical lattice involvement with the anisotropic electron–phonon coupling being on a time scale (1–3.5 ps depending on direction) of the same order of magnitude as that of the spin exchange of electron pairing in the high-temperature superconducting phase.     

The filled skutterudite CeOs4As12: A hybridization gap semiconductor

X-ray diffraction, electrical resistivity, magnetization, specific heat, and thermoelectric power measurements are presented for single crystals of the new filled skutterudite compound CeOs₄As₁₂, which reveal phenomena that are associated with f-electron-conduction electron hybridization. Valence fluctuations or Kondo behavior dominates the physics down to T ~ 135 K. The correlated electron behavior is manifested at low temperatures as a hybridization gap-insulating state. The small energy gap Δ₁/k_B ~ 73 K, taken from fits to electrical resistivity data, correlates with the evolution of a weakly magnetic or nonmagnetic ground state, which is evident in the magnetization data below a coherence temperature T_coh ~ 45 K. Additionally, the low-temperature electronic specific heat coefficient is small, γ ~ 19 mJ/mol K². Some results for the nonmagnetic analogue compound LaOs₄As₁₂ are also presented for comparison purposes.     

The Low-Angle Boundaries Misorientation and Lattice Parameter Changes in the Root of Single-Crystalline CMSX-4 Superalloy Blades

The relationship between the angles of misorientation of macroscopic low-angle boundaries (LABs) and changes in the lattice parameter of the γ′-phase around the LABs in the root of single-crystalline (SX) turbine blades made of CMSX-4 superalloy were studied. The blades with an axial orientation of the [001] type were solidified using an industrial Bridgman furnace with a 3 mm/min withdrawal rate. X-ray diffraction topography, the EFG Ω-scan X-ray diffraction method, scanning electron microscopy, and Laue diffraction were used to study the thin lamellar samples with a thickness of 0.5 mm and orientation of the surface perpendicular to the [001] direction. It is found that in the areas with a width of a few millimetres around LABs, decreases in the lattice parameter of the γ′-phase occur. These lattice parameter changes are related to the internal stresses of the γ′-phase caused by local changes in the concentration of alloying elements and/or to the dendrite bending near the LABs. X-ray topography used on two surfaces of thin lamellar samples coupled with the lattice parameter measurements of the γ′-phase near the LAB allows separating the misorientation component of LAB diffraction contrast from the component and visualising the internal stresses of the γ′-phase.