A guided simulated annealing method for crystallography

Using convolutional neural network denoising to reduce ambiguity in X-ray coherent diffraction imaging

The inherent ambiguity in reconstructed images from coherent diffraction imaging (CDI) poses an intrinsic challenge, as images derived from the same dataset under varying initial conditions often display inconsistencies. This study introduces a method that employs the Noise2Noise approach combined with neural networks to effectively mitigate these ambiguities. We applied this methodology to hundreds of ambiguous reconstructed images retrieved from a single diffraction pattern using a conventional retrieval algorithm. Our results demonstrate that ambiguous features in these reconstructions are effectively treated as inter-reconstruction noise and are significantly reduced. The post-Noise2Noise treated images closely approximate the average and singular value decomposition analysis of various reconstructions, providing consistent and reliable reconstructions.

Oxidation induced strain and defects in magnetite crystals

Oxidation of magnetite (Fe₃O₄) has broad implications in geochemistry, environmental science and materials science. Spatially resolving strain fields and defect evolution during oxidation of magnetite provides further insight into its reaction mechanisms. Here we show that the morphology and internal strain distributions within individual nano-sized (~400 nm) magnetite crystals can be visualized using Bragg coherent diffractive imaging (BCDI). Oxidative dissolution in acidic solutions leads to increases in the magnitude and heterogeneity of internal strains. This heterogeneous strain likely results from lattice distortion caused by Fe(II) diffusion that leads to the observed domains of increasing compressive and tensile strains. In contrast, strain evolution is less pronounced during magnetite oxidation at elevated temperature in air. These results demonstrate that oxidative dissolution of magnetite can induce a rich array of strain and defect structures, which could be an important factor that contributes to the high reactivity observed on magnetite particles in aqueous environment.

Multiresolution phase extension of a trypsin inhibitor structure from 5 A to 2 A based on diffraction amplitudes alone

For a specific structure of trypsin inhibitor, starting from a 5 A phase set, about 80% of the 2 A phases are correctly determined within an error of 18 degrees by applying a multiresolution refinement procedure. The refinement proceeds both in real and reciprocal spaces. In extending the structure from 5 to 2 A, the amplitudes of the reflections are the only requirements for this procedure. In contrast to the conventional phase extension scheme, the amplitudes are used not only in the Fourier synthesis but also in the real-space density modifications.

Three-dimensional GaN-Ga2O3 core shell structure revealed by x-ray diffraction microscopy

In combination of direct phase retrieval of coherent x-ray diffraction patterns with a novel tomographic reconstruction algorithm, we, for the first time, carried out quantitative 3D imaging of a heat-treated GaN particle with each voxel corresponding to 17 x 17 x 17 nm3. We observed the platelet structure of GaN and the formation of small islands on the surface of the platelets, and successfully captured the internal GaN-Ga2O3 core shell structure in three dimensions. This work opens the door for nondestructive and quantitative imaging of 3D morphology and 3D internal structure of a wide range of materials at the nanometer scale resolution that are amorphous or possess only short-range atomic organization.

Coexistence of ferroelectricity and ferromagnetism in tantalum clusters

The atomic and electronic structures of Ta(N) (N=2-23) clusters have been determined in the framework of pseudopotential density-functional calculations, based upon an unbiased global search with guided simulated annealing to an empirical potential. It is found that the ground-state structures of Ta(N) are very similar to those of Nb(N), showing no preference for the icosahedral growth. Also, a size- and structure-dependent ferroelectricity is found in these tantalum clusters. More importantly, it is found that the ferroelectricity and ferromagnetism can coexist in the homogeneous transition-metal cluster, offering a possibility to obtain a new type of "multiferroic" materials composed of the clusters. Finally, the far-infrared spectroscopy is suggested to be an efficient tool to distinguish the ferroelectric clusters.

Possible ground-state structure of Au26: A highly symmetric tubelike cage

The stable tubelike Au(N) (N=26-28) has been found using the scalar relativistic all-electron density functional theory calculations, which becomes another powerful candidate for the lowest-energy Au(N), competing in energy with those space-filled structures suggested previously. Unlike the icosahedral "golden" fullerene Au32, these tubelike gold clusters may be closely related to the synthesized single-wall gold nanotubes (SWGNTs). The ground-state Au26 has a hollow tubelike structure constructed from the (6, 0) SWGNT, yielding a high-symmetry D6d cage, based upon which the most stable Au27 and Au28 can be obtained by adding one and two more capped atoms on its one end, respectively.

Improved Monte Carlo sampling in a real space approach to the crystallographic phase problem

A real space approach has been proposed to solve the x-ray phase problem formulated as a minimization problem. The cost function consists of two parts: one represents the usual crystallographical residual while the other enforces the probability distribution of the invariant phase triplets. Starting from a random real space structure, the atoms are moved one by one to gradually reduce the cost function (simulated annealing). In addition, the atoms are encouragd to preferentially sample the high density regions in space determined by an approximate density map which in turn is updated and modified by averaging and Fourier synthesis. Such a reduction of the configurational space has led to considerable improvement of the algorithm compared to an earlier version. Trial calculations for structures including hexadecaisoleucinomycin (HEXIL) and a collagenlike peptide (PPG) are presented.