Figure 1-1. Brief illustration of difference between 3D electron tomography and Brownian one-particle reconstruction in (a) image acquisition step and (b) 3D... 16

Figure 2-1. In-situ TEM images of ligand-protected Pt nanoparticles in GLC. (a) Five consecutive TEM images before averaging of eight nanocrystals. (b) Weighted... 35

Figure 2-2. Isosurfaces of high-resolution 3D density maps (a), atomic position maps (b), and strain (εxx) maps (c) of eight individual nanoparticles (particles 1 to 8)....[이미지참조] 36

Figure 2-3. Fourier shell correlation (FSC) between a 3D density map from odd-frames and a map from even-frames. (a to f) Single crystalline particles, (g) a particle... 37

Figure 2-4. (a) 3D density maps and (b) atomic position maps of eight Pt nanoparticles with the zone axis of (top) [100], (middle) [110], and (bottom) [111].... 38

Figure 2-5. Sliced images of the density map (white mesh) and the atomic coordinates (red points) of Particle 4. Scale bar, 1 nm. 39

Figure 2-6. Representative sliced images of colored density map and allocated atomic positions (black points) of Particle 4. 40

Figure 2-7. Six components of 3D strain tensors of eight reconstructed Pt nanoparticles. Strain is indicated by color gradient from blue (-5%), white (0%) to... 41

Figure 2-8. 3D reconstruction using simulated TEM images from a 2.5 nm-sized Pt nanocrystal having ideal fcc coordinate. (a) Representative simulated TEM images.... 42

Figure 2-9. 3D reconstruction using simulated TEM images from a 4.0 nm-sized Pt nanocrystal having ideal fcc coordinate. (a) Representative simulated TEM images.... 43

Figure 2-10. 3D reconstruction using simulated TEM images followed by binning. (a to h) 3D reconstruction of model Pt nanoparticles with sizes of (a to d) 2.5 nm and... 44

Figure 2-11. 3D reconstruction using simulated TEM images of Pt nanoparticles in graphene liquid cells with a thickness of 10 nm. (a and e) Atomic models of Pt... 45

Figure 2-12. 3D reconstruction using simulated TEM images of Pt nanoparticles in graphene liquid cells with a thickness of 10 nm. Images are followed by binning. (a... 46

Figure 2-13. Comparison between (top) original TEM images, (middle) reprojected images (simple sum), and (bottom) multi-slice simulated images from the eight Pt... 47

Figure 2-14. Representative intensity profiles of representative raw TEM images and simulated images by multi-slice simulation. 48

Figure 2-15. Comparison between reconstruction results from the original TEM images and re-reconstruction results. (a, c, e, and g) 3D density maps overlaid with... 49

Figure 2-16. Orientation coverage allocated onto xy- planes. Orientation coverage plots of (a to f) Single crystalline particles, (g) particle with distorted crystal, and (h)... 50

Figure 2-17. 3D reconstruction using simulated TEM images with random defocus. (a) Simulated TEM images obtained from multi-slice simulation of a model Pt... 51

Figure 2-18. The representative results of leave-one-out cross-validation (LOOCV). Mean square error (MSE) curve versus standard deviation of Gaussian kernel for the... 52

Figure 2-19. 3D density maps and atomic positions of particle 4 along the [100] (a), [110] (b), and [111] (c) zone axes. Scale bar, 1 nm. 53

Figure 2-20. Detailed atomic structure analysis of single-crystalline Pt nanoparticles in liquid. (a) Packing structure of the nanocrystal. A, B, and C represent repeating... 54

Figure 2-21. Depth profile of coordination numbers in reconstructed Particle 4. 55

Figure 2-22. Size-dependent properties of Pt nanocrystals inferred from their 3D atomic maps. (a and b) Fitted lattice parameters (a) and averaged radial strain values... 56

Figure 2-23. Sliced images of the radial strain map (εrr) of Particle 4. Strain is indicated by color gradient from red (5%), white (0%) to blue (-5%) colors.[이미지참조] 57

Figure 2-24. DFT calculation of ligand adsorption energies at Pt surfaces. (a) Different adsorption sites of binding units of PVP ligand on different facets of Pt.... 58

Figure 2-25. 3D structure analysis of nanocrystals that have complicated structures. (a to c) 3D structure analysis of a distorted nanocrystal (particle 7). The overall... 59

Figure 2-26. Sliced maps of the six components of the 3D strain tensors for a single- crystalline particle (particle 4). Strain is indicated by the color scale. Scale bar, 1 nm. 60

Figure 2-27. Histograms of the strain tensors of all atoms (top), core atoms (middle), and surface atoms (bottom) of particle 4. 61

Figure 2-28. Sliced maps of the six components of the strain tensors for a particle with a distorted lattice (particle 7). Strain is indicated by the color scale. Scale bar, 1 nm. 62

Figure 2-29. Histograms of the strain tensors of all atoms (top), core atoms (middle), and surface atoms (bottom) of particle 7. 63

Figure 2-30. Displacement fields for each atomic position of Particle 4. Displacement is indicated by color gradient from red (0.5 Å), white (0 Å) to blue (-... 64

Figure 2-31. Six components of strain tensors of (a) the single crystalline particle (Particle 4) and (b) distorted particle (Particle 7). Strain maps in top panels were... 65

Figure 2-32. Correlation between size and tensile strains of single crystalline nanocrystals (Particle 1 to 6). (a) Strains of all constituent atoms, (b) strains of core... 66

Figure 2-33. 3D reconstruction of nanoparticles with other elements. (a and d) Simulated TEM images obtained from multi-slice simulation of (a) a model 2.5 nm-... 67

Figure 3-1. Overall workflow of SINGLE. 78

Figure 3-2. Tracking of individual nanocrystal trajectories. Tracking results of particle 1 (a-b) and 2 (c-d) throughout the movie (blue to red). Representative time... 79

Figure 3-3. Tracking results of particle 1 throughout the movie by using previous (top) and new code (bottom). 80

Figure 3-4. Schematic depiction of the graphene subtraction procedure. (a) Graphene peak identification and subtraction. An average background spectrum is... 81

Figure 3-5. Time-restrained 2D clustering. (a) Fraction of angular change throughout the time series. Red dashed line is the trend line. Projection directions are... 82

Figure 3-6. 3D reconstruction results and atomic level structure analysis. (a to c) 3D density maps (a), radial strain maps from fitted atomic coordinates (b), and their slice... 83

Figure 3-7. Validation of 3D reconstructions. (a) 3D reconstruction of simulated disordered particle with known atomic structure. Left: Model of a disordered... 84

Figure 3-8. Simulated TEM images with different liquid thicknesses. (a) TEM simulation results of Pt nanocrystal in graphene liquid cells with different liquid... 85

Figure 4-1. Quantitative symmetry analysis from 3D atomic structures. (a) Scheme for symmetry distance (CSM) calculation from an atomic position map. (b) Plots... 98

Figure 4-2. CSM calculation results from model structure. CSM from nanocrystal with ideal fcc unit cell (a), nanocrystal with monoclinic unit cell (b), and icosahedron... 99

Figure 4-3. Symmetry maps of six previously reported nanoparticles. colored with CSM value for all six types of symmetry. Scale bar, 1 nm. 100

Figure 4-4. Plots between CSM values for six different types of symmetries and radial distance of each atom from the center of mass. 101

Figure 4-5. Symmetry analysis by using modeled structure with random distortion. (a) Atomic position map. (b) Plots between radial position and CSM values for... 102

Figure 4-6. Procedure of symmetrizing. (a) rotational symmetry and (b) mirror symmetry. (1) Folding points by rotation with 2πi/n radians (n-fold rotational... 103

Figure 4-7. Correlations between types of symmetries. 104

Figure 4-8. DFT calculation for specific symmetry breakage. (a) Four model systems deformed in certain system direction while preserving others. (b) Energy... 105

Figure 4-9. Correlations between CSM values from distortion in the uniaxial direction. 106

Figure 4-10. Symmetry analysis results from six particles. (a) Symmetry maps of six platinum nanoparticles reconstructed via Brownian one particle reconstruction,... 107

Figure 4-11. CSM profile of atoms with coordination number 12 (not surface atoms). Relationships between CSM values for different particles and different types of... 108

Figure 4-12. Histograms of CSM values from six particles. (a) Histograms of CSM values from particles without internal symmetry breakage. (b) Histograms of CSM... 109

Figure 4-13. Integrated histograms of CSM from six particles. Data are collected from six types of symmetries of all atomic points consisting of six platinum single... 110

Figure 4-14. Relationship between symmetry breakage and particle properties. (a) Correlation between averaged lattice parameter and averaged CSM value (3- fold... 111

Figure 4-15. Correlations between types of structure descriptors. 112

Figure 5-1. Overview of 3D reconstruction of multi-element nanoparticles. Ord ered and disordered multi-element nanoparticles follow different pathways to... 125

Figure 5-2. 1D modelling for single-element, ordered multi-element, and disorde red multi-element systems. Unit cell structures, 1D models and their intensity... 126

Figure 5-3. Comparison between simulated TEM images of fcc Pt and disordered- fcc FePt. (a) Simulated TEM images of Pt and FePt nanoparticles and their 2D power... 127

Figure 5-4. Comparison between experimental TEM images of fcc Pt and disordered-fcc FePt. Experimental TEM images of Pt (e) and FePt (f) nanoparticles,... 128

Figure 5-5. Comparison between simulated TEM images with liquid background and without the background. Simulated TEM images of multi-element nanoparti... 129

Figure 5-6. 3D reconstruction of ordered multi-element nanoparticle using simulated TEM images without liquid noise removal. (a) Ground truth atomic stru... 130

Figure 5-7. 3D reconstruction of disordered multi-element nanoparticle using simulated TEM images without liquid noise removal. (a) Ground truth atomic stru... 131

Figure 5-8. 3D reconstruction process for ordered multi-element nanoparticles. (top row: rocksalt PbSe, middle row: zinc blende CdSe, bottom row: wurtzite CdSe) (a)... 132

Figure 5-9. Atomic structures obtained from 3D Coulomb density maps with atom type classification. The reconstructed atomic structures are compared with the... 133

Figure 5-10. Slices of 3D atomic maps of ground truth and reconstructed atomic structures for PbSe and CdSe. 134

Figure 5-11. Validation of 3D reconstruction of ordered multi-element (PbSe and CdSe) nanoparticles. (a) Comparison between original projection images (simulated... 135

Figure 5-12. 3D reconstruction results using two-step reconstruction of ordered multi-element nanoparticles (rocksalt PbSe, wurtzite CdSe, and zinc blende CdSe).... 136

Figure 5-13. 3D reconstruction results for ordered rock-salt PbSe using different low-pass limits. (a) 3D Coulomb density maps. As the low-pass limit increases (more... 137

Figure 5-14. 3D reconstruction of 3 nm-sized ordered rocksalt PbSe nanoparticle. (a) The ground truth atomic structure. Yellow and green spheres correspond... 138

Figure 5-15. 3D reconstruction process for disordered multi-element nanoparticles. (a) Input atomic structures. Grey and orange spheres correspond to Pt and F... 139

Figure 5-16. Representative slices of 3D atomic maps of ground truth structures and reconstructed structures. Root mean square displacement (RMSD) between input... 140

Figure 5-17. Slices of 3D atomic maps of ground truth and reconstructed atomic structures of four FePt nanoparticles. 141

Figure 5-18. 3D reconstruction results from the 1st step. Cutoff low-pass threshold of (2.7 Å)-1 was used for the first step. Scale bar, 1 nm.[이미지참조] 142

Figure 5-19. Validation of 3D reconstruction of four disordered multi-element nanoparticles. (a) Comparison between original projection images (simulated TE... 143

Figure 5-20. 3D reconstruction result using single-step reconstruction of disordered fcc Fe71Pt238. (a) 3D Coulomb density map. Used initial model and applied low-pass... 144

Figure 5-21. 3D reconstruction result of disordered fcc Fe71Pt238 with different low-pass filters. (a) 3D Coulomb density maps. Applied low-pass filter filters are...[이미지참조] 145

Figure 5-22. 3D reconstruction of 3 nm-sized disordered fcc FePt nanoparticle. (a) The ground truth atomic structure. Grey and orange spheres correspond to Pt... 146