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Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses
Facilitating the very short and intense pulses from an X-ray laser for the purpose of imaging small bioparticles carries the potential for structure determination at atomic resolution without the need for crystallization. In this study, we explore experimental strategies for this idea based on data collected at the Linac Coherent Light Source from 40 nm virus particles injected into a hard X-ray beam.
The Physics of Gain Mechanisms in a Self-Amplified Spontaneous Emission Free-Electron Laser
This is the final report for the DoE BES contract DE-FG02-07ER46272. This grant began under a title that gives its history in a few words: The Physics of Gain Mechanisms in a Self-Amplified Spontaneous Emission Free-Electron Laser. At the time of adopting this name, the UCLA Particle Beam Physics Laboratory (PBPL) was at the forefront of the first demonstrations of SASE FEL, giving the experimental basis for the 4th generation X-ray light source now exemplified by the LCLS, a remarkable generation of machines that have revolutionize nanoscale and ultrafast science. The grant title indicates that physical aspects of the FEL are of interest, and implies that progress requires comprehensive investigations. These aspects include: the physics and technology of high brightness electron beam generation, phase space manipulations, advanced beam diagnostics, state-of-the-art undulators, studies of FEL mode characteristics, as well as the introduction of new theoretical models and start-to-end simulations, all yielding a deep understanding of the SASE FEL. The latest period (2010-13) of BES grant support has been the most productive yet for the UCLA PBPL, and the extensive list of accomplishments is illustrative of our central contributions to advanced FEL research. We give a concise overview here and review our research results in further detail below. In FEL and ultrafast beam physics, we have experimentally investigated: production of helical beams and FEL modes with orbital angular momentum; chirp-taper single-spike FEL gain; new FROG techniques optimized for FEL, introduced coherent imaging of beam profiles using transition radiation; and demonstrated a next generation cryoundulator. We have performed deep theoretical studies of these phenomena and other advanced FEL physics concepts, such as the space-charge amplifier. In high brightness beams, we have: introduced a new class of hybrid photoinjector for <100 fs beam production; developed new approaches to self-shaped ellipsoidal beams; used nonlinear plasma oscillations to create beam pulse trains; tested new plasmonic, high quantum efficiency cathodes, and developed new methods of beam measurement with um spatial/sub-fs temporal resolution. In ultrafast imaging, we have: developed advanced electro-optic timing systems, performed the 1st pump-probe study using single shot UED, demonstrated continuously time-resolved UED with RF deflection; made initial use of inverse Compton scattering (ICS) X-ray sources in application through single-shot inline phase contrast imaging, established single-shot X-ray diffraction, and observed ICS high harmonic generation and redshifting due to nonlinear effects. In 5th generation light source research, we have developed the techniques of narrowband, very high power coherent Cerenkov radiation sources based on dielectric wakefield devices. This work is represented by numerous publications in leading journals: e.g. Nature Physics, Physical Review Letters, Applied Physics Letters. The PBPL program’s influence on the field also extends to organization of the electron beam applications community; we have organized the first international UED workshops and the initial two meetings dedicated to 5th generation light source.
Correlations in Scattered X-Ray Laser Pulses Reveal Nanoscale Structural Features of Viruses
We use extremely bright and ultrashort pulses from an x-ray free-electron laser (XFEL) to measure correlations in x rays scattered from individual bioparticles. This allows us to go beyond the traditional crystallography and single-particle imaging approaches for structure investigations. We employ angular correlations to recover the three-dimensional (3D) structure of nanoscale viruses from x-ray diffraction data measured at the Linac Coherent Light Source. Correlations provide us with a comprehensive structural fingerprint of a 3D virus, which we use both for model-based and ab initio structure recovery. The analyses reveal a clear indication that the structure of the viruses deviates from the expected perfect icosahedral symmetry. Lastly, our results anticipate exciting opportunities for XFEL studies of the structure and dynamics of nanoscale objects by means of angular correlations.
Correlative image learning of chemo-mechanics in phase-transforming solids
We report constitutive laws underlie most physical processes in nature. However, learning such equations in heterogeneous solids (for example, due to phase separation) is challenging. One such relationship is between composition and eigenstrain, which governs the chemo-mechanical expansion in solids. Here we developed a generalizable, physically constrained image-learning framework to algorithmically learn the chemo-mechanical constitutive law at the nanoscale from correlative four-dimensional scanning transmission electron microscopy and X-ray spectro-ptychography images. We demonstrated this approach on Li X FePO 4 , a technologically relevant battery positive electrode material. We uncovered the functional form of the composition–eigenstrain relation in this two-phase binary solid across the entire composition range (0 ≤ X ≤ 1), including inside the thermodynamically unstable miscibility gap. The learned relation directly validates Vegard’s law of linear response at the nanoscale. Our physics-constrained data-driven approach directly visualizes the residual strain field (by removing the compositional and coherency strain), which is otherwise impossible to quantify. Heterogeneities in the residual strain arise from misfit dislocations and were independently verified by X-ray diffraction line profile analysis. Our work provides the means to simultaneously quantify chemical expansion, coherency strain and dislocations in battery electrodes, which has implications on rate capabilities and lifetime. Broadly, this work also highlights the potential of integrating correlative microscopy and image learning for extracting material properties and physics.
The phase-contrast imaging instrument at the matter in extreme conditions endstation at LCLS
Here, we describe the phase-contrast imaging instrument at the Matter in Extreme Conditions (MEC) endstation of the Linac Coherent Light Source. The instrument can image phenomena with a spatial resolution of a few hundreds of nanometers and at the same time reveal the atomic structure through X-ray diffraction, with a temporal resolution better than 100 fs. It was specifically designed for studies relevant to high-energy-density science and can monitor, e.g., shock fronts, phase transitions, or void collapses. This versatile instrument was commissioned last year and is now available to the MEC user community.
Imaging in real and reciprocal space at the Diamond beamline I13
The Diamond Imaging and Coherence beamline I13 consists of two independent branchlines for imaging in real and reciprocal space. Different microscopies are available providing a range of spatial resolution from 5µm to potentially 5nm. The beamline operates in the energy range of 6-35keV covering different scientific areas such as biomedicine, materials science and geophysics. Several original devices have been developed at the beamline, such as the EXCALIBUR photon counting detector and the combined robot arms for coherent X-ray diffraction.
Diffractive Imaging of Conical Intersections Amplified by Resonant Infrared Fields
The fate of virtually all photochemical reactions is determined by conical intersections. These are energetically degenerate regions of molecular potential energy surfaces that strongly couple electronic states, thereby enabling fast relaxation channels. Their direct spectroscopic detection relies on weak features that are often buried beneath stronger, less interesting contributions. For azobenzene photoisomerization, a textbook photochemical reaction, we demonstrate how a resonant infrared field can be employed during the conical intersection passage to significantly enhance its coherence signatures in time-resolved Xray diffraction while leaving the product yield intact. Furthermore, this transition-state amplification holds promise to bring signals of conical intersections above the detection threshold.
Complex-valued universal linear transformations and image encryption using spatially incoherent diffractive networks
As an optical processor, a diffractive deep neural network (D2NN) utilizes engineered diffractive surfaces designed through machine learning to perform all-optical information processing, completing its tasks at the speed of light propagation through thin optical layers. With sufficient degrees of freedom, D2NNs can perform arbitrary complex-valued linear transformations using spatially coherent light. Similarly, D2NNs can also perform arbitrary linear intensity transformations with spatially incoherent illumination; however, under spatially incoherent light, these transformations are nonnegative, acting on diffraction-limited optical intensity patterns at the input field of view. Here, we expand the use of spatially incoherent D2NNs to complex-valued information processing for executing arbitrary complex-valued linear transformations using spatially incoherent light. Through simulations, we show that as the number of optimized diffractive features increases beyond a threshold dictated by the multiplication of the input and output space-bandwidth products, a spatially incoherent diffractive visual processor can approximate any complex-valued linear transformation and be used for all-optical image encryption using incoherent illumination. The findings are important for the all-optical processing of information under natural light using various forms of diffractive surface-based optical processors.
Unravelling surface and interfacial structures of a metal–organic framework by transmission electron microscopy
Metal-organic frameworks (MOFs) are crystalline porous materials with designable topology, porosity and functionality, having promising applications in gas storage and separation, ion conduction and catalysis. It is challenging to observe MOFs with transmission electron microscopy (TEM) due to the extreme instability of MOFs upon electron beam irradiation. We use a direct-detection electron-counting camera to acquire TEM images of the MOF ZIF-8 with an ultralow dose of 4.1 electrons per square ångström to retain the structural integrity. The obtained image involves structural information transferred up to 2.1 Å, allowing the resolution of individual atomic columns of Zn and organic linkers in the framework. Furthermore, TEM reveals important local structural features of ZIF-8 crystals that cannot be identified by diffraction techniques, including armchair-type surface terminations and coherent interfaces between assembled crystals. Our observations allow us to understand how ZIF-8 crystals self-assemble and the subsequent influence of interfacial cavities on mass transport of guest molecules.
Ultrafast Imaging of Molecules with Electron Diffraction
Photoexcited molecules convert light into chemical and mechanical energy through changes in electronic and nuclear structure that take place on femtosecond timescales. Gas phase ultrafast electron diffraction (GUED) is an ideal tool to probe the nuclear geometry evolution of the molecules and complements spectroscopic methods that are mostly sensitive to the electronic state. GUED is a passive probing tool that does not alter the molecular properties during the probing process and is sensitive to the spatial distribution of charge in the molecule, including both electrons and nuclei. Improvements in temporal resolution have enabled GUED to capture coherent nuclear motions in molecules in the excited and ground electronic states with femtosecond and subangstrom resolution. Here we present the basic theory of GUED and explain what information is encoded in the diffraction signal, review how GUED has been used to observe coherent structural dynamics in recent experiments, and discuss the advantages and limitations of the method.
Projective imaging of high-energy nuclei via coherent exclusive vector meson production in electron-nucleus collisions
One of the major goals of modern nuclear experiments is to study the distributions of gluons inside nuclei at high energy. A key measurement is the coherent exclusive vector meson (VM) production in diffractive electron-nucleus collisions, where the gluon spatial distribution inside the nucleus can be obtained through a Fourier transform of the squared nuclear momentum transfer (|t|) distribution. This research aims to overcome the two main obstacles of the |t| measurement: limited precision in measuring |t| arising from the momentum resolution of the outgoing electron and the overwhelming incoherent background. We demonstrate that by measuring the projected |t| distribution along the direction perpendicular to the electron scattering plane, the effect of the outgoing electron’s momentum resolution can be effectively mitigated, and the diffractive pattern is largely restored. Furthermore, we propose to measure the angular distribution of the VM’s decay daughters to statistically remove the incoherent background.
Strain Localization during Diametral Compression of ZrO{sub 2}(Y{sub 2}O{sub 3}) Ceramics
Deformation behavior of ZrO{sub 2}−Y{sub 2}O{sub 3} ceramics under conditions of diametral compression has been studied by method of digital image correlation. Spatiotemporal patterns of strain localization along the axis of a deformed sample (ε{sub xx}(x)) and across this axis (ε{sub yy}(y)) were obtained. It is established that the ε{sub xx} and ε{sub yy} deformations accumulated during the diametral compression test are inhomogeneously distributed over the sample. This is manifested by variation of the microstructure characteristics such as the size of the coherently diffracting domains of a tetragonal phase and microstresses and leads to the tetragonal–monoclinic phase transformation. This pattern of strain localization is correlated with the observed inhomogeneity of microstresses arising in the material volume.
Tuning Li-Ion Diffusion in α-LiMn 1– x Fe x PO 4 Nanocrystals by Antisite Defects and Embedded β-Phase for Advanced Li-Ion Batteries
Olivine-structured LiMn1-xFexPO4 has become a promising candidate for cathode materials owing to its higher working voltage of 4.1 V and thus larger energy density than that of LiFePO4, which has been used for electric vehicles batteries with the advantage of high safety but disadvantage of low energy density due to its lower working voltage of 3.4 V. One drawback of LiMn1-xFexPO4 electrode is its relatively low electronic and Li-ionic conductivity with Li-ion one-dimensional diffusion. Herein, olivine-structured α-LiMn0.5Fe0.5PO4 nanocrystals were synthesized with optimized Li-ion diffusion channels in LiMn1-xFexPO4 nanocrystals by inducing high concentrations of Fe2+-Li+ antisite defects, which showed impressive capacity improvements of approaching 162, 127, 73, and 55 mAh g-1 at 0.1, 10, 50, and 100 C, respectively, and a long-term cycling stability of maintaining about 74% capacity after 1000 cycles at 10 C. By using high-resolution transmission electron microscopy imaging and joint refinement of hard X-ray and neutron powder diffraction patterns, we revealed that the extraordinary high-rate performance could be achieved by suppressing the formation of electrochemically inactive phase (β-LiMn1-xFexPO4, which is first reported in this work) embedded in α-LiMn0.5Fe0.5PO4. Because of the coherent orientation relationship between β- and α- phases, the β-phase embedded would impede the Li+ diffusion along the [100] and/or [001] directions that was activated by the high density of Fe2+-Li+ antisite (4.24%) in α-phase. Thus, by optimizing concentrations of Fe2+-Li+ antisite defects and suppressing β-phase-embedded olivine structure, Li-ion diffusion properties in LiMn1-xFexPO4 nanocrystals can be tuned by generating new Li+ tunneling. These findings may provide insights into the design and generation of other advanced electrode materials with improved rate performance.
Imaging of sub-wavelength structures radiating coherently near microspheres
Using a two-dimensional model, we show that the optical images of a sub-wavelength object depend strongly on the excitation of its electromagnetic modes. There exist modes that enable the resolution of the object features smaller than the classical diffraction limit, in particular, due to the destructive interference. We propose to use such modes for super-resolution of resonant structures such as coupled cavities, metal dimers, or bowties. A dielectric microsphere in contact with the object forms its magnified image in a wide range of the virtual image plane positions. It is also suggested that the resonances may significantly affect the resolution quantification in recent experimental studies.
Imaging Nanoscale Energy Transport and Conversion with Ultrafast Electron Microscopy (Final Technical Report)
Light-matter interactions are ubiquitous in nature and reside at the heart of innumerable technologies. The cascade of processes that occur when a material absorbs a photon of light are exceedingly complex and are interwoven in both space and time, rendering precise determination of the atomic-scale and ultrafast mechanisms immensely challenging. The advent of methods for generating short pulses of light several decades ago led to major advances in understanding the initial moments of light absorption and the resultant effects, though directly interrogating the response of the atoms within the material continued to prove challenging. More recently, methods for generating ultrashort pulses of X-rays and fast electrons have opened the way to probing photoinduced structural dynamics of a wide range of matter in multiple phases. An especially promising laboratory-scale method is ultrafast electron microscopy (UEM), wherein the modalities of conventional transmission electron microscopes (imaging, diffraction, spectroscopy) are extended into the femtosecond temporal regime. Here, the ultrafast imaging and diffraction modalities of UEM were used to study the transient structural aspects of photoexcitation of semiconducting materials (e.g., spatially-resolved electron-phonon coupling, excitation and emission of acoustic phonons, and discrete nanoscale scattering processes). The project had three main objectives: (1) determination of the excitation mechanisms of dense, hypersonic charge-carrier waves and the spatially mediated means by which they couple to the lattice via coherent phonon emission, especially with UEM imaging, wherein effects of nanoscale structural and morphological features on the coupling and relaxation dynamics are expected to dictate nucleation sites and preferred wave vectors, (2) elucidation of photoinduced acoustic-phonon seeding, emergence, propagation, and decay over nanoscale crystal regions and especially with respect to local strain fields and atomic-scale disruptions in lattice order, and (3) interwoven with the first two were efforts aimed at realizing combined angstrom-femtosecond spatiotemporal imaging with UEM. The outcomes and impacts of this project were the generation of new knowledge with respect to fundamental light-matter interactions and, especially, the spatially-mediated excitation and evolution of the structural response of materials following coherent photoexcitation. Importantly, the spatial and temporal resolutions of the UEM imaging modalities used are well-suited for such studies and enable spatially-resolved mechanisms to be determined as a function of atomic order, structural features, and morphology. In addition, ultrafast crystallographic measurements were used to correlate real- and reciprocal-space dynamics in order to determine atomic-scale preferential wave vectors and ultrafast scattering mechanisms, especially as dictated by specimen boundary conditions. The obtained results, as detailed in peer-reviewed publications and presentations, illustrate the importance of ultrafast, angstrom-scale real-space imaging for developing a comprehensive understanding of energy transport and conversion in materials.
Structural Changes as a Function of Thickness in [(SnSe) 1+δ ] m TiSe 2 Heterostructures
Single- and few-layer metal chalcogenide compounds are of significant interest due to structural changes and emergent electronic properties on reducing dimensionality from three to two dimensions. To explore dimensionality effects in SnSe, a series of [(SnSe) 1+δ ] m TiSe 2 intergrowth structures with increasing SnSe layer thickness (m = 1-4) were prepared from designed thin-film precursors. In-plane diffraction patterns indicated that significant structural changes occurred in the basal plane of the SnSe constituent as m is increased. Scanning transmission electron microscopy cross-sectional images of the m = 1 compound indicate long-range coherence between layers, whereas the m >/= 2 compounds show extensive rotational disorder between the constituent layers. For m >/= 2, the images of the SnSe constituent contain a variety of stacking sequences of SnSe bilayers. Density functional theory calculations suggest that the formation energy is similar for several different SnSe stacking sequences. The compounds show unexpected transport properties as m is increased, including the first p-type behavior observed in (MSe)m(TiSe 2 ) n compounds. The resistivity of the m >/- 2 compounds is larger than for m = 1, with m = 2 being the largest. At room temperature, the Hall coefficient is positive for m = 1 and negative for m = 2-4. The Hall coefficient of the m = 2 compound changes sign as temperature is decreased. The room-temperature Seebeck coefficient, however, switches from negative to positive at m = 3. These properties are incompatible with single band transport indicating that the compounds are not simple composites.
Airy light-sheet Raman imaging
Light-sheet fluorescence microscopy has greatly improved the speed and overall photostability of optically sectioning cellular and multi-cellular specimens. Similar gains have also been conferred by light-sheet Raman imaging; these schemes, however, rely on diffraction limited Gaussian beams that hinder the uniformity and size of the imaging field-of-view, and, as such, the resulting throughput rates. Here, we demonstrate that a digitally scanned Airy beam increases the Raman imaging throughput rates by more than an order of magnitude than conventional diffraction-limited beams. Overall, this, spectrometer-less, approach enabled 3D imaging of microparticles with high contrast and 1 µm axial resolution at 300 msec integration times per plane and orders of magnitude lower irradiation density than coherent Raman imaging schemes. We detail the apparatus and its performance, as well as its compatibility with fluorescence light-sheet and quantitative-phase imaging towards rapid and low phototoxicity multimodal imaging.