Perfect crystals are rare in nature. Real materials often contain crystal defects and chemical order/disorder such as grain boundaries, dislocations, interfaces, surface reconstructions and point defects. Such disruption in periodicity strongly affects material properties and functionality. Despite rapid development of quantitative material characterization methods, correlating three-dimensional (3D) atomic arrangements of chemical order/disorder and crystal defects with material properties remains a challenge. On a parallel front, quantum mechanics calculations such as density functional theory (DFT) have progressed from the modelling of ideal bulk systems to modelling 'real' materials with dopants, dislocations, grain boundaries and interfaces; but these calculations rely heavily on average atomic models extracted from crystallography. To improve the predictive power of first-principles calculations, there is a pressing need to use atomic coordinates of real systems beyond average crystallographic measurements. Here we determine the 3D coordinates of 6,569 iron and 16,627 platinum atoms in an iron-platinum nanoparticle, and correlate chemical order/disorder and crystal defects with material properties at the single-atom level. We identify rich structural variety with unprecedented 3D detail including atomic composition, grain boundaries, anti-phase boundaries, anti-site point defects and swap defects. We show that the experimentally measured coordinates and chemical species with 22 picometre precision can be used as direct input for DFT calculations of material properties such as atomic spin and orbital magnetic moments and local magnetocrystalline anisotropy. This work combines 3D atomic structure determination of crystal defects with DFT calculations, which is expected to advance our understanding of structure-property relationships at the fundamental level.

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 1-3. 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. Over the years, a number of experimental and computational methods have been used to investigate nucleation processes 4-17 , but it remains unachievable to experimentally determine the 3D atomic structure and dynamics of early stage nuclei. Here, we develop 4D atomic electron tomography (AET) to study early stage nucleation at 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 a few atoms 2 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 are corroborated by molecular dynamics simulations of heterogeneous and homogeneous nucleation in liquid-solid phase transitions of Pt. Our experimental and molecular dynamics results differ from classical nucleation theory (CNT) 1,2,18 , indicating a theory beyond CNT is needed to describe early stage nucleation at the atomic scale. Looking forward, we anticipate that 4D AET opens the door to study many fundamental problems in materials science, nanoscience, condensed matter physics and chemistry such as phase transition, atomic diffusion, grain boundary dynamics, interface motion, defect dynamics and surface reconstruction with 4D atomic resolution. AET is a powerful method to determine the 3D atomic structure of materials without the assumption of crystallinity 19 and has been applied to study dislocations, stacking faults, grain boundaries, atomic displacement, strain tensor, chemical order/disorder and point defects with unprecedented 3D detail 20-26. But all of these studies were of static structures. To probe the 4D atomic structure of early stage nucleation, we have tracked the same nuclei at different times and applied AET to determine their 3D atomic coordinates and species at each time (Methods). We used FePt nanoparticles as a model system because binary alloys have been widely used to study phase transitions 2 and FePt is a very promising material for next generation magnetic recording media 25,27. As-synthesized FePt nanoparticles form a chemically disordered face-centred cubic (fcc) structure (A1 phase) 27. With annealing, the A1 phase Author contributions J.M. conceived and directed the project; F.S. and H.Z. prepared the samples; J.Z.,

Multi-elemental alloy nanoparticles (MEA-NPs) hold great promise for catalyst discovery in a virtually unlimited compositional space. However, rational and controllable synthesize of these intrinsically complex structures remains a challenge. Here, we report the computationally aided, entropy-driven design and synthesis of highly efficient and durable catalyst MEA-NPs. The computational strategy includes prescreening of millions of compositions, prediction of alloy formation by density functional theory calculations, and examination of structural stability by a hybrid Monte Carlo and molecular dynamics method. Selected compositions can be efficiently and rapidly synthesized at high temperature (e.g., 1500 K, 0.5 s) with excellent thermal stability. We applied these MEA-NPs for catalytic NH 3 decomposition and observed outstanding performance due to the synergistic effect of multielemental mixing, their small size, and the alloy phase. We anticipate that the computationally aided rational design and rapid synthesis of MEA-NPs are broadly applicable for various catalytic reactions and will accelerate material discovery. Computationally aided, entropy-driven synthesis of highly efficient and durable multi-elemental alloy catalysts.(11), eaaz0510. 6 Sci Adv ARTICLE TOOLS

Amorphous solids such as glass are ubiquitous in our daily life and have found broad applications ranging from window glass and solar cells to telecommunications and transformer cores 1,2 . However, due to the lack of long-range order, the threedimensional (3D) atomic structure of amorphous solids have thus far defied any direct experimental determination 3-12 . Here, using a multi-component metallic glass as a model, we advance atomic electron tomography to determine its 3D atomic positions and chemical species with a precision of 21 picometer. We quantify the short-range order (SRO) and medium-range order (MRO) of the 3D atomic arrangement. We find that although the 3D atomic packing of the SRO is geometrically disordered, some SROs connect with each other to form crystal-like

Summary. Background: To avoid pathological platelet aggregation by von Willebrand factor (VWF), VWF multimers are regulated in size and reactivity for adhesion by ADAMTS13-mediated proteolysis in a shear flow dependent manner. Objective and methods: We examined whether tensile stress in VWF under shear flow activates the VWF A2 domain for cleavage by ADAMTS13 using molecular dynamics simulations. We generated a full length mutant VWF featuring a homologous disulfide bond in A2 (N1493C and C1670S), in an attempt to lock A2 against unfolding. Results: We indeed observed stepwise unfolding of A2 and exposure of its deeply buried ADAMTS13 cleavage site. Interestingly, disulfide bonds in the adjacent and highly homologous VWF A1 and A3 domains obstruct their mechanical unfolding. We find this mutant A2 (N1493C and C1670S) to feature ADAMTS13-resistant behavior in vitro. Conclusions: Our results yield molecular-detail evidence for the force-sensing function of VWF A2, by revealing how tension in VWF due to shear flow selectively exposes the A2 proteolysis site to ADAMTS13 for cleavage while keeping the folded remainder of A2 intact and functional. We find the unconventional ÔknottedÕ Rossmann fold of A2 to be the key to this mechanical response, tailored for regulating VWF size and activity. Based on our model we discuss the pathomechanism of some natural mutations in the VWF A2 domain that significantly increase the cleavage by ADAMTS13 without shearing or chemical denaturation, and provide with the cleavage-activated A2 conformation a structural basis for the design of inhibitors for VWF type 2 diseases.

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. Here, we present the mathematical implementation of a tomographic algorithm, termed GENeralized Fourier Iterative REconstruction (GENFIRE), for high-resolution 3D reconstruction from a limited number of 2D projections. GENFIRE first assembles a 3D Fourier grid with oversampling and then iterates between real and reciprocal space to search 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 through numerical simulations and by experimentally 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.

The renewable electricity-driven electrocatalytic oxidation of biomass represents a pathway to produce value-added chemicals from waste biomass such as glycerol (a byproduct of industrial biodiesel production). However, it remains difficult to design an efficient electrocatalyst with explicit structure–property relationships. Herein, we report a single-atom bismuth (Bi)-doping strategy to endow Co3O4 with enhanced activity and selectivity toward electrocatalytic glycerol oxidation reaction (GOR). Experimental characterizations and theoretical calculations reveal that single-atom Bi substitutes cobalt at octahedral sites (CoOh 3+) in Co3O4, facilitating the generation of reactive hydroxyl species (OH*) at adjacent tetrahedral Co sites (CoTd 2+). Mechanism studies demonstrate that OH* accelerates the oxidation of hydroxyl groups and carbon–carbon (C–C) bond cleavage, achieving GOR activity (400 mA cm–2 at 1.446 V vs reversible hydrogen electrode, RHE) and high faradaic efficiency of formate (97.05 ± 2.55%). Our study shows a promising way to promote the electro-oxidation activity of spinel oxides for biomass valorization by a single-atom doping strategy.

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 a novel medium-range order, named the pentagonal bipyramid network. 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 2 the study of the amorphous-crystalline phase transition and glass transition at the single-atom level.In 1952, Frank hypothesized that icosahedral order is the prevalent atomic motif in monatomic liquids 1 . Over the past six decades, there have been a great deal of experimental, computational, and theoretical studies to understand the structure of liquids and amorphous materials [2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17][18][19][20][21] . A polytetrahedral packing model was proposed to explain the 3D atomic structure of monatomic liquids and amorphous materials 22 , in which icosahedral order is a key feature. The icosahedral order has also been found to play a critical role in the structure of metallic glasses and quasicrystals [23][24][25][26][27][28][29] . Despite all these developments, however, no experimental method could directly determine the 3D atomic packing of liquids and amorphous materials due to the lack of long-range order. Atomic electron tomography (AET), allowing the determination of 3D atomic structure of materials without assuming crystallinity 30 , is uniquely positioned to address this challenge. Since its first demonstration in 2012 31 , AET has been applied to reveal a wide range of crystal defects in materials such as grain boundaries, dislocations, stacking faults, point defects, atomic ripples, bond distortion, strain tensors and chemical order/disorder in three and four dimensions 30,[32][33][34][35][36][37][38][39] . More recently, AET was used to determine the structure of a multi-component glass-forming nanoparticle and quantitatively characterize the short-and medium-range order of its 3D atomic arrangement 40 . Here we advance AET to reveal the 3D atomic structure of an amorphous Ta thin film and two amorphous Pd nanoparticles that are not metallic glasses but liquid-like solids. We observe that pentagonal bipyramids are the main atomic motifs in the monatomic amorphous materials. Instead of assembling icosahedra, most pentagonal bipyramids closely connect