Joseph P. Robinson

Structure of photosystem II and substrate binding at room temperature.

Light-induced oxidation of water by photosystem II (PS II) in plants, algae and cyanobacteria has generated most of the dioxygen in the atmosphere. PS II, a membrane-bound multi-subunit pigment protein complex, couples the one-electron photochemistry at the reaction centre with the four-electron redox chemistry of water oxidation at the Mn4CaO5 cluster in the oxygen-evolving complex (OEC). Under illumination, the OEC cycles through five intermediate S-states (S0 to S4), in which S1 is the dark-stable state and S3 is the last semi-stable state before O–O bond formation and O2 evolution. A detailed understanding of the O–O bond formation mechanism remains a challenge, and will require elucidation of both the structures of the OEC in the different S-states and the binding of the two substrate waters to the catalytic site. Here we report the use of femtosecond pulses from an X-ray free electron laser (XFEL) to obtain damage-free, room temperature structures of dark-adapted (S1), two-flash illuminated (2F; S3-enriched), and ammonia-bound two-flash illuminated (2F-NH3; S3-enriched) PS II. Although the recent 1.95 Å resolution structure of PS II at cryogenic temperature using an XFEL provided a damage-free view of the S1 state, measurements at room temperature are required to study the structural landscape of proteins under functional conditions, and also for in situ advancement of the S-states. To investigate the water-binding site(s), ammonia, a water analogue, has been used as a marker, as it binds to the Mn4CaO5 cluster in the S2 and S3 states. Since the ammonia-bound OEC is active, the ammonia-binding Mn site is not a substrate water site. This approach, together with a comparison of the native dark and 2F states, is used to discriminate between proposed O–O bond formation mechanisms.

Diffractive imaging of a rotational wavepacket in nitrogen molecules with femtosecond megaelectronvolt electron pulses

Imaging changes in molecular geometries on their natural femtosecond timescale with sub-Angström spatial precision is one of the critical challenges in the chemical sciences, as the nuclear geometry changes determine the molecular reactivity. For photoexcited molecules, the nuclear dynamics determine the photoenergy conversion path and efficiency. Here we report a gas-phase electron diffraction experiment using megaelectronvolt (MeV) electrons, where we captured the rotational wavepacket dynamics of nonadiabatically laser-aligned nitrogen molecules. We achieved a combination of 100 fs root-mean-squared temporal resolution and sub-Angstrom (0.76 Å) spatial resolution that makes it possible to resolve the position of the nuclei within the molecule. In addition, the diffraction patterns reveal the angular distribution of the molecules, which changes from prolate (aligned) to oblate (anti-aligned) in 300 fs. Our results demonstrate a significant and promising step towards making atomically resolved movies of molecular reactions.

Families in the Wild (FIW): Large-Scale Kinship Image Database and Benchmarks

We present the largest kinship recognition dataset to date, Families in the Wild (FIW). Motivated by the lack of a single, unified dataset for kinship recognition, we aim to provide a dataset that captivates the interest of the research community. With only a small team, we were able to collect, organize, and label over 10,000 family photos of 1,000 families with our annotation tool designed to mark complex hierarchical relationships and local label information in a quick and efficient manner. We include several benchmarks for two image-based tasks, kinship verification and family recognition. For this, we incorporate several visual features and metric learning methods as baselines. Also, we demonstrate that a pre-trained Convolutional Neural Network (CNN) as an off-the-shelf feature extractor outperforms the other feature types. Then, results were further boosted by fine-tuning two deep CNNs on FIW data: (1) for kinship verification, a triplet loss function was learned on top of the network of pre-train weights; (2) for family recognition, a family-specific softmax classifier was added to the network.

Visualization of nanocrystal breathing modes at extreme strains.

Nanoscale dimensions in materials lead to unique electronic and structural properties with applications ranging from site-specific drug delivery to anodes for lithium-ion batteries. These functional properties often involve large-amplitude strains and structural modifications, and thus require an understanding of the dynamics of these processes. Here we use femtosecond X-ray scattering techniques to visualize, in real time and with atomic-scale resolution, light-induced anisotropic strains in nanocrystal spheres and rods. Strains at the percent level are observed in CdS and CdSe samples, associated with a rapid expansion followed by contraction along the nanosphere or nanorod radial direction driven by a transient carrier-induced stress. These morphological changes occur simultaneously with the first steps in the melting transition on hundreds of femtosecond timescales. This work represents the first direct real-time probe of the dynamics of these large-amplitude strains and shape changes in few-nanometre-scale particles.

Recent development of thin diamond crystals for X-ray FEL beam-sharing

The recent success of the X-ray Free Electron Lasers has generated great interests from the user communities of a wide range of scientific disciplines including physics, chemistry, structural biology and material science, creating tremendous demand on FEL beamtime access. Due to the serial nature of FEL operation, various beam-sharing techniques have been investigated in order to potentially increase the FEL beamtime capacity. Here we report the recent development in using thin diamond single crystals for spectrally splitting the FEL beam at the Linac Coherent Light Source, thus potentially allowing the simultaneous operation of multiple instruments. Experimental findings in crystal mounting and its thermal performance, position and pointing stabilities of the reflected beam, and impact of the crystal on the FEL transmitted beam profile are presented.

Real-Time Visualization of Nanocrystal Solid–Solid Transformation Pathways

Measurement and understanding of the microscopic pathways materials follow as they transform is crucial for the design and synthesis of new metastable phases of matter. Here we employ femtosecond single-shot X-ray diffraction techniques to measure the pathways underlying solid-solid phase transitions in cadmium sulfide nanorods, a model system for a general class of martensitic transformations. Using picosecond rise-time laser-generated shocks to trigger the transformation, we directly observe the transition state dynamics associated with the wurtzite-to-rocksalt structural phase transformation in cadmium sulfide with atomic-scale resolution. A stress-dependent transition path is observed. At high peak stresses, the majority of the sample is converted directly into the rocksalt phase with no evidence of an intermediate prior to rocksalt formation. At lower peak stresses, a transient five-coordinated intermediate structure is observed consistent with previous first principles modeling.

Kinship Verification on Families in the Wild with Marginalized Denoising Metric Learning

With our Families In the Wild (FIW) dataset, which consists of labels 1, 000 families in over 12, 000 family photos, we benchmarked the largest kinship verification experiment to date. FIW, with its quality data and labels for full family trees found worldwide, more accurately is the true, global distribution of blood relatives with a total 378, 300 face pairs of 9 different relationship types. This gives support to tackle the problem with modern-day data-driven methods, which are imperative due to the complex nature of tasks involving visual kinship recognition– many hidden factors and less discrimination when considering face pairs of blood relatives. For this, we propose a denoising auto-encoder based robust metric learning (DML) framework and its marginalized version (mDML) to explicitly preserve the intrinsic structure of data and simultaneously endow the discriminative information into the learned features. Large-scale experiments show that our method outperforms other features and metric based approaches on each of the 9 relationship types.

Femtosecond optical/hard X-ray timing diagnostics at an FEL: implementation and performance

The development of Free Electron Lasers has opened the possibility to investigate ultrafast processes using femtosecond hard x-ray pulses. In optical/x-ray light pump/probe experiments, however, the time resolution is mainly limited by the ability to synchronize both light sources over a long distance (<100 fs FWHM) rather than their pulse length (<10 fs FWHM). We have implemented a spectrally encoding x-ray to optical laser timing diagnostic into the XPP beamline at LCLS with a timing uncertainty down to 10 fs. An x-ray induced change of refractive index in a solid target is temporally probed for single pulses by a chirped white light pulse [4]. By resorting single shot data to the timestamps obtained by the diagnostics, the temporal data quality can be improved to basically pulse length limited time resolution. By interchangable targets and adjustable x-ray and laser foci, the method was successfully applied for very different x-ray parameters. These are different photon energies in the range of 6-20 keV, which at LCLS also includes application of 3rd Harmonic radiation, pulse energy, and bandwidth, when using a Si(111) monochromator.

Three-photon fluorescence imaging of melanin with a dual-wedge confocal scanning system

Confocal microscopy can be used as a practical tool in non-invasive applications in medical diagnostics and evaluation. In particular, it is being used for the early detection of skin cancer to identify pathological cellular components and, potentially, replace conventional biopsies. The detection of melanin and its spatial location and distribution plays a crucial role in the detection and evaluation of skin cancer. Our previous work has shown that the visible emission from melanin is strong and can be easily observed with a near-infrared CW laser using low power. This is due to a unique step-wise, (SW) three-photon excitation of melanin. This paper shows that the same SW, 3-photon fluorescence can also be achieved with an inexpensive, continuous-wave laser using a dual-prism scanning system. This demonstrates that the technology could be integrated into a portable confocal microscope for clinical applications. The results presented here are in agreement with images obtained with the larger and more expensive femtosecond laser system used earlier.

Computational Model of Optical Scattering by Elastin in Lung

Little is understood about the detailed micromechanical properties of lung in vivo. Attempts to improve imaging are hampered by heterogeneity of the tissue. One common ex vivo technique is optical coherence tomography (OCT). Simulated OCT with a Finite-Difference Time-Domain (FDTD) computer model elucidates the relationship between captured images and the physical geometry of the lung. Parallel computation and improved processing power make accurate coherent imaging models feasible. A previous FDTD model of pulsed laser wave propagation in the lung produced images that displayed many of the properties of experimental images. The model was improved with the addition of elastin and increased computational volume. Elastin plays an important role in the simulation because the combination of its fibrous structure and high index of refraction acts as an excellent scatterer of light. This strong scattering increases the signal reported by the simulated OCT scan in areas where elastin is most abundant, improving visualization of the structure as more light is reflected back from the heterogeneous elastin network. However, scattering by elastin decreases the depth of penetration and leads to images that are more difficult to interpret. Gaining a better understanding of how lung structures affect light propagation will lead to improved signal processing, instrumentation, and the development of new probing techniques. This image modeling technique can also be applied to other imaging modalities such as confocal and other laser scanning methods.