GENFIRE: A generalized Fourier iterative reconstruction algorithm for high-resolution 3D imaging

Tomography has made a radical impact on diverse fields ranging from the study of 3D atomic arrangements in matter to the study of human health in medicine. Despite its very diverse applications, the core of tomography remains the same, that is, a mathematical method must be implemented to reconstruct the 3D structure of an object from a number of 2D projections. In many scientific applications, however, the number of projections that can be measured is limited due to geometric constraints, tolerable radiation dose and/or acquisition speed. Thus it becomes an important problem to obtain the best-possible reconstruction from a limited number of projections. Here, we present the mathematical implementation of a tomographic algorithm, termed GENeralized Fourier Iterative REconstruction (GENFIRE). By iterating between real and reciprocal space, GENFIRE searches for a global solution that is concurrently consistent with the measured data and general physical constraints. The algorithm requires minimal human intervention and also incorporates angular refinement to reduce the tilt angle error. We demonstrate that GENFIRE can produce superior results relative to several other popular tomographic reconstruction techniques by numerical simulations, and by experimentally by reconstructing the 3D structure of a porous material and a frozen-hydrated marine cyanobacterium. Equipped with a graphical user interface, GENFIRE is freely available from our website and is expected to find broad applications across different disciplines.Comment: 18 pages, 6 figure

Capturing Nucleation at 4D Atomic Resolution

Nucleation plays a critical role in many physical and biological phenomena ranging from crystallization, melting and evaporation to the formation of clouds and the initiation of neurodegenerative diseases. However, nucleation is a challenging process to study in experiments especially in the early stage when several atoms/molecules start to form a new phase from its parent phase. Here, we advance atomic electron tomography to study early stage nucleation at 4D atomic resolution. Using FePt nanoparticles as a model system, we reveal that early stage nuclei are irregularly shaped, each has a core of one to few atoms with the maximum order parameter, and the order parameter gradient points from the core to the boundary of the nucleus. We capture the structure and dynamics of the same nuclei undergoing growth, fluctuation, dissolution, merging and/or division, which are regulated by the order parameter distribution and its gradient. These experimental observations differ from classical nucleation theory (CNT) and to explain them we propose the order parameter gradient (OPG) model. We show the OPG model generalizes CNT and energetically favours diffuse interfaces for small nuclei and sharp interfaces for large nuclei. We further corroborate this model using molecular dynamics simulations of heterogeneous and homogeneous nucleation in liquid-solid phase transitions of Pt. We anticipate that the OPG model is applicable to different nucleation processes and our experimental method opens the door to study the structure and dynamics of materials with 4D atomic resolution.Comment: 42 pages, 5 figures, 12 supplementary figures and one supplementary tabl

Janus icosahedral particles: amorphization driven by three-dimensional atomic misfit and edge dislocation compensation

Icosahedral nanoparticles composed of fivefold twinned tetrahedra have broad applications. The strain relief mechanism and angular deficiency in icosahedral multiply twinned particles are poorly understood in three dimensions. Here, we resolved the three-dimensional atomic structures of Janus icosahedral nanoparticles using atomic resolution electron tomography. A geometrically fivefold face consistently corresponds to a less ordered face like two hemispheres. We quantify rich structural variety of icosahedra including bond orientation order, bond length, strain tensor; and packing efficiency, atom number, solid angle of each tetrahedron. These structural characteristics exhibit two-sided distribution. Edge dislocations near the axial atoms and small disordered domains fill the angular deficiency. Our findings provide new insights how the fivefold symmetry can be compensated and the geometrically-necessary internal strains relived in multiply twinned particles.Comment: 30 pages, 5 figure

Direct observation of 3D atomic packing in monatomic amorphous materials

Liquids and solids are two fundamental states of matter. However, due to the lack of direct experimental determination, our understanding of the 3D atomic structure of liquids and amorphous solids remained speculative. Here we advance atomic electron tomography to determine for the first time the 3D atomic positions in monatomic amorphous materials, including a Ta thin film and two Pd nanoparticles. We observe that pentagonal bipyramids are the most abundant atomic motifs in these amorphous materials. Instead of forming icosahedra, the majority of pentagonal bipyramids arrange into networks that extend to medium-range scale. Molecular dynamic simulations further reveal that pentagonal bipyramid networks are prevalent in monatomic amorphous liquids, which rapidly grow in size and form icosahedra during the quench from the liquid state to glass state. The experimental method and results are expected to advance the study of the amorphous-crystalline phase transition and glass transition at the single-atom level

Multimodal x-ray and electron microscopy of the Allende meteorite.

Multimodal microscopy that combines complementary nanoscale imaging techniques is critical for extracting comprehensive chemical, structural, and functional information, particularly for heterogeneous samples. X-ray microscopy can achieve high-resolution imaging of bulk materials with chemical, magnetic, electronic, and bond orientation contrast, while electron microscopy provides atomic-scale spatial resolution with quantitative elemental composition. Here, we combine x-ray ptychography and scanning transmission x-ray spectromicroscopy with three-dimensional energy-dispersive spectroscopy and electron tomography to perform structural and chemical mapping of an Allende meteorite particle with 15-nm spatial resolution. We use textural and quantitative elemental information to infer the mineral composition and discuss potential processes that occurred before or after accretion. We anticipate that correlative x-ray and electron microscopy overcome the limitations of individual imaging modalities and open up a route to future multiscale nondestructive microscopies of complex functional materials and biological systems

Deciphering chemical order/disorder and material properties at the single-atom level

Correlating 3D arrangements of atoms and defects with material properties and functionality forms the core of several scientific disciplines. Here, we determined the 3D coordinates of 6,569 iron and 16,627 platinum atoms in a model iron-platinum nanoparticle system to correlate 3D atomic arrangements and chemical order/disorder with material properties at the single-atom level. We identified rich structural variety and chemical order/disorder including 3D atomic composition, grain boundaries, anti-phase boundaries, anti-site point defects and swap defects. We show for the first time that experimentally measured 3D atomic coordinates and chemical species with 22 pm precision can be used as direct input for first-principles calculations of material properties such as atomic magnetic moments and local magnetocrystalline anisotropy. This work not only opens the door to determining 3D atomic arrangements and chemical order/disorder of a wide range of nanostructured materials with high precision, but also will transform our understanding of structure-property relationships at the most fundamental level.Comment: 21 pages, 4 figure

OMECDN: A Password-Generation Model Based on an Ordered Markov Enumerator and Critic Discriminant Network

At present, static text passwords are still the most widely-used identity authentication method. Password-generation technology can generate large-scale password sets and then detect the defects in password-protection mechanisms, which is of great significance for evaluating password-guessing algorithms. However, the existing password-generation technology cannot ignore low-quality passwords in the generated password set, which will lead to low-efficiency password guessing. In this paper, a password-generation model based on an ordered Markov enumerator and critic discriminant network (OMECDN) is proposed, where passwords are generated via an ordered Markov enumerator (OMEN) and a discriminant network according to the probability of the combination of passwords. OMECDN optimizes the performance of password generation with a discriminative network based on the good statistical properties of OMEN. Moreover, the final password set is formed by the selected passwords with a higher score than the preset threshold, which guarantees the superiority of the hit rate of almost all ranges of combinations of passwords over the initial password set. Finally, the experiments show that OMECDN achieves a qualitative improvement in hit rate metrics. In particular, regarding the generation of 107 passwords on the RockYou dataset, the matching entries of the password set generated by the OMECDN model are 25.18% and 243.58% higher than those generated by the OMEN model and the PassGAN model, respectively

Analyzing the correlation among the five indications of the regenerative effectiveness of expanded skin: A retrospective study of 277 expansion cases

Background: Skin expansion is a useful method for harvesting extra tissue. However, the outcome is hardly predictable. Methods: A total of 158 patients with 277 expanded skin cases were reviewed and evaluated via photographs. The review and evaluation were conducted to determine the skin’s regenerative condition. The overall texture of the expanded skin, which was deemed good, fair, or poor, was evaluated. The occurrence of five indications of the limitation of skin regeneration (thinning, color change, stretch marks, varicose vessels, and skin lesions) during expansion was recorded. The correlation between the five indications and the overall texture was statistically analyzed. Results: Among the 277 retrospectively reviewed expansion cases, the occurrence rate of skin deterioration showed significant differences between the expansion sites (P<0.01). Skin deterioration was most commonly seen on the neck and at the back. The occurrence of each indication varied among locations. The odds ratios of color change, stretch marks, varicose vessels, thinning, and skin lesions between good and poor skin conditions were 44.97, 5.09, 22.26, 89.79, and 4.61, respectively (all P<0.001). Conclusion: Skin color, stretch marks, varicose vessels, thickness, and skin lesions are closely correlated with the skin regenerative capacity. An integrated evaluation can help predict the regenerative capacity of expanded skin