Time-resolved crystallography captures light-driven DNA repair.

Photolyase is an enzyme that uses light to catalyze DNA repair. To capture the reaction intermediates involved in the enzyme's catalytic cycle, we conducted a time-resolved crystallography experiment. We found that photolyase traps the excited state of the active cofactor, flavin adenine dinucleotide (FAD), in a highly bent geometry. This excited state performs electron transfer to damaged DNA, inducing repair. We show that the repair reaction, which involves the lysis of two covalent bonds, occurs through a single-bond intermediate. The transformation of the substrate into product crowds the active site and disrupts hydrogen bonds with the enzyme, resulting in stepwise product release, with the 3' thymine ejected first, followed by the 5' base.

Mapping nanocrystal orientations via scanning Laue diffraction microscopy for multi-peak Bragg coherent diffraction imaging.

The recent commissioning of a movable monochromator at the 34-ID-C endstation of the Advanced Photon Source has vastly simplified the collection of Bragg coherent diffraction imaging (BCDI) data from multiple Bragg peaks of sub-micrometre scale samples. Laue patterns arising from the scattering of a polychromatic beam by arbitrarily oriented nanocrystals permit their crystal orientations to be computed, which are then used for locating and collecting several non-co-linear Bragg reflections. The volumetric six-component strain tensor is then constructed by combining the projected displacement fields that are imaged using each of the measured reflections via iterative phase retrieval algorithms. Complications arise when the sample is heterogeneous in composition and/or when multiple grains of a given lattice structure are simultaneously illuminated by the polychromatic beam. Here, a workflow is established for orienting and mapping nanocrystals on a substrate of a different material using scanning Laue diffraction microscopy. The capabilities of the developed algorithms and procedures with both synthetic and experimental data are demonstrated. The robustness is verified by comparing experimental texture maps obtained with Laue diffraction microscopy at the beamline with maps obtained from electron back-scattering diffraction measurements on the same patch of gold nanocrystals. Such tools provide reliable indexing for both isolated and densely distributed nanocrystals, which are challenging to image in three dimensions with other techniques.

Dynamic Tilting of Ferroelectric Domain Walls Caused by Optically Induced Electronic Screening.

Optical excitation perturbs the balance of phenomena selecting the tilt orientation of domain walls within ferroelectric thin films. The high carrier density induced in a low-strain BaTiO_{3} thin film by an above-band-gap ultrafast optical pulse changes the tilt angle that 90° a/c domain walls form with respect to the substrate-film interface. The dynamics of the changes are apparent in time-resolved synchrotron x-ray scattering studies of the domain diffuse scattering. Tilting occurs at 298 K, a temperature at which the a/b and a/c domain phases coexist but is absent at 343 K in the better ordered single-phase a/c regime. Phase coexistence at 298 K leads to increased domain-wall charge density, and thus a larger screening effect than in the single-phase regime. The screening mechanism points to new directions for the manipulation of nanoscale ferroelectricity.

Combining Laue diffraction with Bragg coherent diffraction imaging at 34-ID-C.

Measurement modalities in Bragg coherent diffraction imaging (BCDI) rely on finding a signal from a single nanoscale crystal object which satisfies the Bragg condition among a large number of arbitrarily oriented nanocrystals. However, even when the signal from a single Bragg reflection with (hkl) Miller indices is found, the crystallographic axes on the retrieved three-dimensional (3D) image of the crystal remain unknown, and thus localizing in reciprocal space other Bragg reflections becomes time-consuming or requires good knowledge of the orientation of the crystal. Here, the commissioning of a movable double-bounce Si (111) monochromator at the 34-ID-C endstation of the Advanced Photon Source is reported, which aims at delivering multi-reflection BCDI as a standard tool in a single beamline instrument. The new instrument enables, through rapid switching from monochromatic to broadband (pink) beam, the use of Laue diffraction to determine crystal orientation. With a proper orientation matrix determined for the lattice, one can measure coherent diffraction patterns near multiple Bragg peaks, thus providing sufficient information to image the full strain tensor in 3D. The design, concept of operation, the developed procedures for indexing Laue patterns, and automated measuring of Bragg coherent diffraction data from multiple reflections of the same nanocrystal are discussed.

Nanosecond Optically Induced Phase Transformation in Compressively Strained BiFeO_{3} on LaAlO_{3}.

Above-band-gap optical illumination of compressively strained BiFeO_{3} induces a transient reversible transformation from a state of coexisting tilted tetragonal-like and rhombohedral-like phases to an untilted tetragonal-like phase. Time-resolved synchrotron x-ray diffraction reveals that the transformation is induced by an ultrafast optically induced lattice expansion that shifts the relative free energies of the tetragonal-like and rhombohedral-like phases. The transformation proceeds at interfaces between regions of the tetragonal-like phase and regions of a mixture of tilted phases, consistent with the motion of a phase boundary. The optically induced transformation demonstrates that there are new optically driven routes towards nanosecond-scale control of phase transformations in ferroelectrics and multiferroics.

Photoisomerization Dynamics in a Densely Packed Optically Transformable Azobenzene Monolayer.

Molecular monolayers that can be reconfigured through the use of external stimuli promise to enable the creation of interfaces with precisely selected dynamically adjustable physical and electronic properties with potential impact ranging from electronics to energy storage. Azobenzene-containing molecular monolayers have multiple stable molecular conformations but face a challenging nanoscale problem associated with understanding the basic mechanisms of reconfiguration. Time-resolved X-ray reflectivity studies show that the reconfiguration of a densely packed rhenium-azobenzene monolayer occurs in a period of many seconds. The degree of reconfiguration from trans to cis forms depends on the integrated UV fluence and has kinetics that are consistent with a mechanism in which the transformation occurs through the nucleation and growth of nanoscale two-dimensional regions of the cis isomer.

Mesoscopic Elastic Distortions in GaAs Quantum Dot Heterostructures.

Quantum devices formed in high-electron-mobility semiconductor heterostructures provide a route through which quantum mechanical effects can be exploited on length scales accessible to lithography and integrated electronics. The electrostatic definition of quantum dots in semiconductor heterostructure devices intrinsically involves the lithographic fabrication of intricate patterns of metallic electrodes. The formation of metal/semiconductor interfaces, growth processes associated with polycrystalline metallic layers, and differential thermal expansion produce elastic distortion in the active areas of quantum devices. Understanding and controlling these distortions present a significant challenge in quantum device development. We report synchrotron X-ray nanodiffraction measurements combined with dynamical X-ray diffraction modeling that reveal lattice tilts with a depth-averaged value up to 0.04° and strain on the order of 10-4 in the two-dimensional electron gas (2DEG) in a GaAs/AlGaAs heterostructure. Elastic distortions in GaAs/AlGaAs heterostructures modify the potential energy landscape in the 2DEG due to the generation of a deformation potential and an electric field through the piezoelectric effect. The stress induced by metal electrodes directly impacts the ability to control the positions of the potential minima where quantum dots form and the coupling between neighboring quantum dots.

Domain alignment within ferroelectric/dielectric PbTiO3/SrTiO3 superlattice nanostructures.

The ferroelectric domain pattern within lithographically defined PbTiO3/SrTiO3 ferroelectric/dielectric heteroepitaxial superlattice nanostructures is strongly influenced by the edges of the structures. Synchrotron X-ray nanobeam diffraction reveals that the spontaneously formed 180° ferroelectric stripe domains exhibited by such superlattices adopt a configuration in rectangular nanostructures in which domain walls are aligned with long patterned edges. The angular distribution of X-ray diffuse scattering intensity from nanodomains indicates that domains are aligned within an angular range of approximately 20° with respect to the edges. Computational studies based on a time-dependent Landau-Ginzburg-Devonshire model show that the preferred direction of the alignment results from lowering of the bulk and electrostrictive contributions to the free energy of the system due to the release of the lateral mechanical constraint. This unexpected alignment appears to be intrinsic and not a result of distortions or defects caused by the patterning process. Our work demonstrates how nanostructuring and patterning of heteroepitaxial superlattices allow for pathways to create and control ferroelectric structures that may appear counterintuitive.

Photoinduced Domain Pattern Transformation in Ferroelectric-Dielectric Superlattices.

The nanodomain pattern in ferroelectric-dielectric superlattices transforms to a uniform polarization state under above-band-gap optical excitation. X-ray scattering reveals a disappearance of domain diffuse scattering and an expansion of the lattice. The reappearance of the domain pattern occurs over a period of seconds at room temperature, suggesting a transformation mechanism in which charge carriers in long-lived trap states screen the depolarization field. A Landau-Ginzburg-Devonshire model predicts changes in lattice parameter and a critical carrier concentration for the transformation.