Search

Scientific data 3, 160064 -(2016). doi:10.1038/sdata.2016.64, Single particle diffractive imaging data from Rice Dwarf Virus (RDV) were recorded using the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS). RDV was chosen as it is a well-characterized model system, useful for proof-of-principle experiments, system optimization and algorithm development. RDV, an icosahedral virus of about 70 nm in diameter, was aerosolized and injected into the approximately 0.1 μm diameter focused hard X-ray beam at the CXI instrument of LCLS. Diffraction patterns from RDV with signal to 5.9 Ångström were recorded. The diffraction data are available through the Coherent X-ray Imaging Data Bank (CXIDB) as a resource for algorithm development, the contents of which are described here., Published by Nature Publ. Group, London

Van der Waals moire materials have emerged as a highly controllable platform to study electronic correlation phenomena1–17. Robust correlated insulating states have recently been discovered at both integer and fractional filling factors of semiconductor moire systems10–17. In this study we explored the thermodynamic properties of these states by measuring the gate capacitance of MoSe2/WS2 moire superlattices. We observed a series of incompressible states for filling factors 0–8 and anomalously large capacitance in the intervening compressible regions. The anomalously large capacitance, which was nearly 60% above the device’s geometrical capacitance, was most pronounced at small filling factors, below the melting temperature of the charge-ordered states, and for small sample–gate separation. It is a manifestation of the device-geometry-dependent Coulomb interaction between electrons and phase mixing of the charge-ordered states. Based on these results, we were able to extract the thermodynamic gap of the correlated insulating states and the device’s electronic entropy and specific heat capacity. Our findings establish capacitance as a powerful probe of the correlated states in semiconductor moire systems and demonstrate control of these states via sample–gate coupling. Measuring the gate capacitance serves as a probe of the correlated states in MoSe2/WS2 moire superlattices, which can be further controlled via sample–gate coupling.

Quantum particles on a lattice with competing long-range interactions are ubiquitous in physics; transition metal oxides1,2, layered molecular crystals3 and trapped-ion arrays4 are a few examples. In the strongly interacting regime, these systems often show a rich variety of quantum many-body ground states that challenge theory2. The emergence of transition metal dichalcogenide moire superlattices provides a highly controllable platform in which to study long-range electronic correlations5-12. Here we report an observation of nearly two dozen correlated insulating states at fractional fillings of tungsten diselenide/tungsten disulfide moire superlattices. This finding is enabled by a new optical sensing technique that is based on the sensitivity to the dielectric environment of the exciton excited states in a single-layer semiconductor of tungsten diselenide. The cascade of insulating states shows an energy ordering that is nearly symmetric about a filling factor of half a particle per superlattice site. We propose a series of charge-ordered states at commensurate filling fractions that range from generalized Wigner crystals7 to charge density waves. Our study lays the groundwork for using moire superlattices to simulate a wealth of quantum many-body problems that are described by the two-dimensional extended Hubbard model3,13,14 or spin models with long-range charge-charge and exchange interactions15,16.

We believe that a necessary first step in understanding the ground state properties of the spin-${\scriptstyle\frac{1}{2}}$ kagome Heisenberg antiferromagnet is a better understanding of this model's very large number of low energy singlet states. A description of the low energy states that is both accurate and amenable for numerical work may ultimately prove to have greater value than knowing only what these properties are, in particular when these turn on the delicate balance of many small energies. We demonstrate how this program would be implemented using the basis of spin-singlet dimerized states, though other bases that have been proposed may serve the same purpose. The quality of a basis is evaluated by its participation in all the low energy singlets, not just the ground state. From an experimental perspective, and again in light of the small energy scales involved, methods that can deliver all the low energy states promise more robust predictions than methods that only refine a fraction of these states., 9 pages, 6 figures, 1 table

In recent years, the success of serial femtosecond crystallography and the paucity of beamtime at X-ray free-electron lasers have motivated the development of serial microcrystallography experiments at storage-ring synchrotron sources. However, especially at storage-ring sources, if a crystal is too small it will have suffered significant radiation damage before diffracting a sufficient number of X-rays into Bragg peaks for peak-indexing software to determine the crystal orientation. As a consequence, the data frames of small crystals often cannot be indexed and are discarded. Introduced here is a method based on the expand–maximize–compress (EMC) algorithm to solve protein structures, specifically from data frames for which indexing methods fail because too few X-rays are diffracted into Bragg peaks. The method is demonstrated on a real serial microcrystallography data set whose signals are too weak to be indexed by conventional methods. In spite of the daunting background scatter from the sample-delivery medium, it was still possible to solve the protein structure at 2.1 Å resolution. The ability of the EMC algorithm to analyze weak data frames will help to reduce sample consumption. It will also allow serial microcrystallography to be performed with crystals that are otherwise too small to be feasibly analyzed at storage-ring sources.

To simulate the signal level of serial microcrystallography experiments at storage ring sources, data frames were collected from a large lysozyme crystal rotated about two orthogonal axes and illuminated by a dim X-ray source. Using the EMC algorithm, this study shows that three-dimensional intensity reconstruction is still feasible even without the knowledge of the crystal orientation in each data frame., Recently, there has been a growing interest in adapting serial microcrystallography (SMX) experiments to existing storage ring (SR) sources. For very small crystals, however, radiation damage occurs before sufficient numbers of photons are diffracted to determine the orientation of the crystal. The challenge is to merge data from a large number of such ‘sparse’ frames in order to measure the full reciprocal space intensity. To simulate sparse frames, a dataset was collected from a large lysozyme crystal illuminated by a dim X-ray source. The crystal was continuously rotated about two orthogonal axes to sample a subset of the rotation space. With the EMC algorithm [expand–maximize–compress; Loh & Elser (2009). Phys. Rev. E, 80, 026705], it is shown that the diffracted intensity of the crystal can still be reconstructed even without knowledge of the orientation of the crystal in any sparse frame. Moreover, parallel computation implementations were designed to considerably improve the time and memory scaling of the algorithm. The results show that EMC-based SMX experiments should be feasible at SR sources.

We introduce a new toy model for the study of glasses: the hard-matrix model (HMM). This may be viewed as a single particle moving on $\mathrm{SO}(N)$, where there is a potential proportional to the 1-norm of the matrix. The ground states of the model are "crystals" where all matrix elements have the same magnitude. These are the Hadamard matrices when $N$ is divisible by four. Just as finding the latter has challenged mathematicians, our model fails to find them upon cooling and instead shows all the behaviors that characterize physical glasses. With simulations we have located the first-order crystallization temperature, the Kauzmann temperature where the glass would have the same entropy as the crystal, as well as the standard, measurement-time dependent glass transition temperature. Our model also brings to light a new kind of elementary excitation special to the glass phase: the "rubicon". In our model these are associated with the finite density of matrix elements near zero, the maximum in their contribution to the energy. Rubicons enable the system to cross between basins without thermal activation, a possibility not much discussed in the standard landscape picture. We use these modes to explain the slow dynamics in our model and speculate about their role in its quantum extension in the context of many-body localization., 20 pages, 9 figures

The decomposition of a matrix, as a product of factors with particular properties, is a much used tool in numerical analysis. Here we develop methods for decomposing a matrix $C$ into a product $X Y$, where the factors $X$ and $Y$ are required to minimize their distance from an arbitrary pair $X_0$ and $Y_0$. This type of decomposition, a projection to a matrix product constraint, in combination with projections that impose structural properties on $X$ and $Y$, forms the basis of a general method of decomposing a matrix into factors with specified properties. Results are presented for the application of these methods to a number of hard problems in exact factorization., Comment: 37 pages, 8 figures

Using the EMC algorithm, the three-dimensional intensity was successfully reconstructed from millions of non-oriented, sparse data frames collected from a hen egg-white lysozyme crystal rotating about a single axis. The protein structure was solved from the reconstructed intensity. This result is encouraging for the development of synchrotron-based serial microcrystallography., X-ray free-electron lasers (XFELs) have inspired the development of serial femtosecond crystallography (SFX) as a method to solve the structure of proteins. SFX datasets are collected from a sequence of protein microcrystals injected across ultrashort X-ray pulses. The idea behind SFX is that diffraction from the intense, ultrashort X-ray pulses leaves the crystal before the crystal is obliterated by the effects of the X-ray pulse. The success of SFX at XFELs has catalyzed interest in analogous experiments at synchrotron-radiation (SR) sources, where data are collected from many small crystals and the ultrashort pulses are replaced by exposure times that are kept short enough to avoid significant crystal damage. The diffraction signal from each short exposure is so ‘sparse’ in recorded photons that the process of recording the crystal intensity is itself a reconstruction problem. Using the EMC algorithm, a successful reconstruction is demonstrated here in a sparsity regime where there are no Bragg peaks that conventionally would serve to determine the orientation of the crystal in each exposure. In this proof-of-principle experiment, a hen egg-white lysozyme (HEWL) crystal rotating about a single axis was illuminated by an X-ray beam from an X-ray generator to simulate the diffraction patterns of microcrystals from synchrotron radiation. Millions of these sparse frames, typically containing only ∼200 photons per frame, were recorded using a fast-framing detector. It is shown that reconstruction of three-dimensional diffraction intensity is possible using the EMC algorithm, even with these extremely sparse frames and without knowledge of the rotation angle. Further, the reconstructed intensity can be phased and refined to solve the protein structure using traditional crystallographic software. This suggests that synchrotron-based serial crystallography of micrometre-sized crystals can be practical with the aid of the EMC algorithm even in cases where the data are sparse.

Aberration-corrected optics have made electron microscopy at atomic resolution a widespread and often essential tool for characterizing nanoscale structures. Image resolution has traditionally been improved by increasing the numerical aperture of the lens (α) and the beam energy, with the state-of-the-art at 300 kiloelectronvolts just entering the deep sub-angstrom (that is, less than 0.5 angstrom) regime. Two-dimensional (2D) materials are imaged at lower beam energies to avoid displacement damage from large momenta transfers, limiting spatial resolution to about 1 angstrom. Here, by combining an electron microscope pixel-array detector with the dynamic range necessary to record the complete distribution of transmitted electrons and full-field ptychography to recover phase information from the full phase space, we increase the spatial resolution well beyond the traditional numerical-aperture-limited resolution. At a beam energy of 80 kiloelectronvolts, our ptychographic reconstruction improves the image contrast of single-atom defects in MoS2 substantially, reaching an information limit close to 5α, which corresponds to an Abbe diffraction-limited resolution of 0.39 angstrom, at the electron dose and imaging conditions for which conventional imaging methods reach only 0.98 angstrom.

These lectures were prepared for the 2014 PCMI graduate summer school and were designed to be a lightweight introduction to statistical mechanics for mathematicians. The applications feature some of the themes of the summer school: sphere packings and tilings., 43 pages, 8 figures

Single-particle imaging (SPI) with X-ray free-electron lasers has the potential to change fundamentally how biomacromolecules are imaged. The structure would be derived from millions of diffraction patterns, each from a different copy of the macromolecule before it is torn apart by radiation damage. The challenges posed by the resultant data stream are staggering: millions of incomplete, noisy and un-oriented patterns have to be computationally assembled into a three-dimensional intensity map and then phase reconstructed. In this paper, theDragonflysoftware package is described, based on a parallel implementation of the expand–maximize–compress reconstruction algorithm that is well suited for this task. Auxiliary modules to simulate SPI data streams are also included to assess the feasibility of proposed SPI experiments at the Linac Coherent Light Source, Stanford, California, USA.

A figure in the article by Lan, Wierman, Tate, Philipp, Elser & Gruner [J. Appl. Cryst. (2017), 50, 985–993] is corrected.

The problem of reconstructing an object from diffraction data that has been incoherently averaged over a discrete group of symmetries is considered. A necessary condition for such data to uniquely specify the object is derived in terms of the object support and the symmetry group. An algorithm is introduced for reconstructing objects from symmetry-averaged data and its use with simulations is demonstrated. The results demonstrate the feasibility of structure determination using a recent proposal for aligning molecules by means of their anisotropic dielectric interaction with an intense light field

Intense femtosecond x-ray pulses from free-electron laser sources allow the imaging of individual particles in a single shot. Early experiments at the Linac Coherent Light Source (LCLS) have led to rapid progress in the field and, so far, coherent diffractive images have been recorded from biological specimens, aerosols, and quantum systems with a few-tens-of-nanometers resolution. In March 2014, LCLS held a workshop to discuss the scientific and technical challenges for reaching the ultimate goal of atomic resolution with single-shot coherent diffractive imaging. This paper summarizes the workshop findings and presents the roadmap toward reaching atomic resolution, 3D imaging at free-electron laser sources.

An algorithm for determining crystal structures from diffraction data is described which does not rely on the usual Fourier-space formulations of atomicity. The new algorithm implements atomicity constraints in real-space, as well as intensity constraints in Fourier-space, by projections which restore each constraint with the minimal modification of the scattering density. To recover the true density, the two projections are combined into a single operation, the difference map, which is iterated until the magnitude of the density modification becomes acceptably small. The resulting density, when acted upon by a single additional operation, is by construction a density which satisfies both intensity and atomicity constraints. Numerical experiments have yielded solutions for atomic resolution x-ray data sets with over 400 non-hydrogen atoms, as well as for neutron data, where positivity of the density cannot be invoked., Comment: 14 pages, 9 figures

Iterative phase retrieval algorithms typically employ projections onto constraint subspaces to recover the unknown phases in the Fourier transform of an image, or, in the case of x-ray crystallography, the electron density of a molecule. For a general class of algorithms, where the basic iteration is specified by the difference map, solutions are associated with fixed points of the map, the attractive character of which determines the effectiveness of the algorithm. The behavior of the difference map near fixed points is controlled by the relative orientation of the tangent spaces of the two constraint subspaces employed by the map. Since the dimensionalities involved are always large in practical applications, it is appropriate to use random matrix theory ideas to analyze the average-case convergence at fixed points. Optimal values of the gamma parameters of the difference map are found which differ somewhat from the values previously obtained on the assumption of orthogonal tangent spaces., Comment: 15 pages

The most efficient known method for solving certain computational problems is to construct an iterated map whose fixed points are by design the problem's solution. Although the origins of this idea go back at least to Newton, the clearest expression of its logical basis is an example due to Mermin. A contemporary application in image recovery demonstrates the power of the method.