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FIG. 2. Schematic of the cell used for molecular dynamics simulations. The filled circles represent Cl atoms and the open circles represent Si atoms. | train/atomic-layer-etching/simulation-usecase/13/fig_2 | atomic-layer-etching/simulation-usecase/13/fig_2 | molecular-structure-diagram | train | [
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Fig. 1. Electron density difference plots after a) the adsorption of an $\mathbb{F}_2$ molecule on top of an S atom and b) the adsorption of an F atom on top of an S atom of $\mathrm{MoS_2}$ . Red lobules correspond to regions of charge accumulation $(+0.01$ contour) whereas blue lobules correspond to charge deple... | train/atomic-layer-etching/simulation-usecase/2/fig_1 | atomic-layer-etching/simulation-usecase/2/fig_1 | molecular-structure-diagram | train | [
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Fig. 3. a) Initial surface structures containing 6 $\mathrm{SF}_x$ groups in the unit cells; b) Energy profiles for each structure at 100, 300 K, and 500 K; c) Snapshot after 15 ps for the simulation starting for the structure initially having 6 $\mathrm{SF}_3$ groups. | train/atomic-layer-etching/simulation-usecase/2/fig_3 | atomic-layer-etching/simulation-usecase/2/fig_3 | molecular-structure-diagram | train | [
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Fig. 4. Trajectories of F atoms on the surface plane show the dynamics of the different surface groups as a function of temperature. The $\mathrm{MoS_2}$ unit cells contain a) six SF groups, b) six $\mathrm{SF_2}$ groups and c) six $\mathrm{SF_3}$ groups. | train/atomic-layer-etching/simulation-usecase/2/fig_4 | atomic-layer-etching/simulation-usecase/2/fig_4 | molecular-structure-diagram | train | [
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Fig. 6. a) Snapshots of AIMD simulation at $1000\mathrm{K}$ starting from a surface composition having 1 SF group, $10\mathrm{SF}_2$ groups, and $1\mathrm{SF}_3$ group in the unit cell. A desorbed $\mathrm{SF}_3$ species begins to abstract an F atom at $1.715\mathrm{ps}$ to yield an $\mathrm{SF}_4$ molecule... | train/atomic-layer-etching/simulation-usecase/2/fig_6 | atomic-layer-etching/simulation-usecase/2/fig_6 | molecular-structure-diagram | train | [
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Fig. 7. a) Snapshots of AIMD simulation at $1500\mathrm{K}$ started with the final structure reached after 5 ps at $1000\mathrm{K}$ (Fig. 6). b) Total energy (black curve) and smoothed profile (red curve). | train/atomic-layer-etching/simulation-usecase/2/fig_7 | atomic-layer-etching/simulation-usecase/2/fig_7 | molecular-structure-diagram | train | [
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Fig. 9. a) Snapshot of MD simulation (5 ps) for $\mathrm{MoS_2}$ bilayer at $1500~\mathrm{K}$ . There are 12F atoms on the top layer and 12F atoms in the interlayer region. The top layer has a pit defect (3 S and 1 Mo vacancies). b) Trajectories of Mo and F atoms during 10 ps of simulation time within the interlayer... | train/atomic-layer-etching/simulation-usecase/2/fig_9 | atomic-layer-etching/simulation-usecase/2/fig_9 | molecular-structure-diagram | train | [
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Figure 1. (a) Equilibrium bulk geometry of rutile $\mathrm{TiO}_2$ . (b) Relaxed surface slab of $\mathrm{TiO}_2(110)$ . Ti and O atoms are displayed in cyan and red, respectively. | train/atomic-layer-etching/simulation-usecase/20/figure_1 | atomic-layer-etching/simulation-usecase/20/figure_1 | molecular-structure-diagram | train | [
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FIG. 2. Si substrates after Cl deposition MD simulations. (a) Crystalline Si substrate model with a (100) top surface at $300~\mathrm{K}$ after it was exposed to $0.1\mathrm{eVCl}$ atoms with an atomic dose of $0.94\times 10^{15}\mathrm{cm}^{-2}$ in MD simulation. (b) Depth profiles of atomic densities correspond... | train/atomic-layer-etching/simulation-usecase/26/fig_2 | atomic-layer-etching/simulation-usecase/26/fig_2 | molecular-structure-diagram | train | [
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FIG. 6. Atomic configurations and the corresponding atomic-density depth profiles at the end of the first ALE cycle (C1) with the thin Cl layer deposition and $20\mathrm{eV}\mathrm{Ar^{+}}$ ion bombardment. The other conditions are the same as those in Table I. The gray, red, and blue spheres represent Si, Cl, and Ar... | train/atomic-layer-etching/simulation-usecase/26/fig_6 | atomic-layer-etching/simulation-usecase/26/fig_6 | molecular-structure-diagram | train | [
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Fig. 2. Plan view atomistic structures of the bulk phase: (a) $2\times 2\times 1$ supercell of expanded alpha- $\mathrm{Al_2O_3}$ , $\mathrm{Al_{48}O_{72}}$ , (b) amorphous $\mathrm{Al_{48}O_{72}}$ after melt-quenching using AIMD simulation, and (c) amorphous $\mathrm{Al_{48}O_{72}}$ after geometry optimization... | train/atomic-layer-etching/simulation-usecase/29/fig_2 | atomic-layer-etching/simulation-usecase/29/fig_2 | molecular-structure-diagram | train | [
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Fig. 5. Planar views of the $\mathsf{a - Al_2O_3}$ substrate models used to simulate the fluorination reaction by HF, terminated with (a) $-\mathrm{OH}$ , (b) $-\mathrm{CH_3}$ , (c) $-\mathrm{AlF}$ , (d) $-\mathrm{AlF_2}$ , and (e) $-\mathrm{AlF_3}$ . | train/atomic-layer-etching/simulation-usecase/29/fig_5 | atomic-layer-etching/simulation-usecase/29/fig_5 | molecular-structure-diagram | train | [
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Figure 2. Structures of the $\mathrm{Ni}(\mathrm{II})$ and $\mathrm{Cu(I)}$ complexes considered. Only the formates are shown. Respective formamidinates can be found by replacing oxygen atoms with secondary amine groups. The relative stabilities are shown in Figure 3. The dimer and tetramer structures are found to ... | train/atomic-layer-etching/simulation-usecase/31/figure_2 | atomic-layer-etching/simulation-usecase/31/figure_2 | molecular-structure-diagram | train | [
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FIG. 1. The eight initial configurations of $\mathrm{BCl}_3$ molecule considered here to find its most stable geometry when it adsorbed on $\mathrm{Al}_2\mathrm{O}_3(100)$ . The values shown in parentheses indicate their respective adsorption energies (unit: $\mathrm{Kcal / mol}$ ) obtained after geometric optimiza... | train/atomic-layer-etching/simulation-usecase/32/fig_1 | atomic-layer-etching/simulation-usecase/32/fig_1 | molecular-structure-diagram | train | [
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FIG. 2. The atomic electron population changes (a) and bond electron population changes (b) of $\mathrm{BCl}_3 + \mathrm{Al}_2\mathrm{O}_3(100)$ system upon the $\mathrm{BCl}_3$ adsorption (unit: electron charge). The oxygen, aluminum, boron, and chlorine atoms are shown in red, violet, bronze, and green, respectiv... | train/atomic-layer-etching/simulation-usecase/32/fig_2 | atomic-layer-etching/simulation-usecase/32/fig_2 | molecular-structure-diagram | train | [
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FIG. 4. Three different routes for the etching of $\mathrm{Al}_2\mathrm{O}_3$ film, i.e., route 1 (a), route 2 (b), and route 3 (c) where the numbers in the figures indicate their respective etching event sequence. Routes 1 and 2 are for ALET processes while route 3 is for conventional plasma etching process. | train/atomic-layer-etching/simulation-usecase/32/fig_4 | atomic-layer-etching/simulation-usecase/32/fig_4 | molecular-structure-diagram | train | [
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Figure 3. (a) Comparison of the DFT and NNP energies along the NNP MD trajectory for the crystalline slab after the primitive training and (b) the etched surface after the NNP MD simulation. (b) | train/atomic-layer-etching/simulation-usecase/33/figure_3 | atomic-layer-etching/simulation-usecase/33/figure_3 | molecular-structure-diagram | train | [
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Figure 8. (a–f) The etched surfaces of $\mathrm{a - Si_3N_4}$ with regard to the angle of incidence $(\theta_{\mathrm{in}})$ of HF: $\theta_{\mathrm{in}} = 0, 15, 30, 45, 60$ and $75^{\circ}$ , respectively. The kinetic energy of the HF molecule is $50~\mathrm{eV}$ . The initial height of the surface before etc... | train/atomic-layer-etching/simulation-usecase/33/figure_8 | atomic-layer-etching/simulation-usecase/33/figure_8 | molecular-structure-diagram | train | [
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Figure 2. Lateral and front views of the PS surface model used in the calculations. Brown spheres represent carbon atoms, and white spheres represent hydrogen atoms. | train/atomic-layer-etching/simulation-usecase/35/FIG2 | atomic-layer-etching/simulation-usecase/35/FIG2 | molecular-structure-diagram | train | [
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] | [{"panel_id":"a","text":"This panel shows a dense, three-dimensional molecular model of bulk polystyrene. Many polymer chains are packed together, forming an entangled network. Individual chains are hard to distinguish at this scale."},{"panel_id":"b","text":"A local segment of the polystyrene network is highlighted an... | [{"panel_id":"a","text":""},{"panel_id":"b","text":""},{"panel_id":"c","text":""}] | [{"panel_id":"a","items":[{"question_type":"Process-Oriented","questions":"","answer_type":"Paragraph","answer":"The bulk structure is very dense and visually complex. Extracting a local segment removes interference from neighboring chains. This allows the intrinsic chain geometry to be examined clearly. It also makes ... | [
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train/atomic-layer-etching/simulation-usecase/35/FIG3 | atomic-layer-etching/simulation-usecase/35/FIG3 | molecular-structure-diagram | train | [
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... | [{"panel_id":"a","text":"The structure shows the intact molecular backbone with a single oxygen added at an isolated site. The overall geometry remains unchanged."},{"panel_id":"b","text":"A second oxygen binds near the first site, causing a small local rearrangement but no global distortion."},{"panel_id":"c","text":"... | [{"panel_id":"a","text":""},{"panel_id":"b","text":""},{"panel_id":"c","text":""},{"panel_id":"d","text":""},{"panel_id":"e","text":""},{"panel_id":"f","text":""},{"panel_id":"g","text":""},{"panel_id":"h","text":""},{"panel_id":"i","text":""},{"panel_id":"j","text":""},{"panel_id":"k","text":""},{"panel_id":"l","text"... | [{"panel_id":"j","items":[{"question_type":"Comparative/Trend","questions":"","answer_type":"Factoid","answer":"Oxygen incorporation increases from six to ten."}]},{"panel_id":"q","items":[{"question_type":"Application/Performance","questions":"","answer_type":"Paragraph","answer":"It provides candidate intermediates o... | [
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0 Figure 6. Optimized geometries of one and two oxygen atoms adsorbed on partially dehydrogenated PS surfaces, expressed as a function of the hydrogen removal coverage $\theta$ . Brown, white, and red spheres represent carbon, hydrogen, and oxygen atoms, respectively. | train/atomic-layer-etching/simulation-usecase/35/FIG6 | atomic-layer-etching/simulation-usecase/35/FIG6 | molecular-structure-diagram | train | [
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Figure 7. (a-d) Snapshots representing the final configurations of oxygen adsorption on partially dehydrogenated PS, for a hydrogen removal coverage of $\theta = 0.48$ . The oxygen flux density and corresponding initial forces are listed below each picture. The graph shows the depth reached by the incoming oxygen atom... | train/atomic-layer-etching/simulation-usecase/35/FIG7 | atomic-layer-etching/simulation-usecase/35/FIG7 | molecular-structure-diagram | train | [
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Fig. 2 (a) Side view of Ge surface after chlorination with different energies. The layer thickness showing here is around $16\mathrm{\AA}$ . Non-adsorbed Cl/Cl $_2$ away from surface have been deleted. (b) System energy (including both kinetic and potential energy) after equilibration (error bar smaller than the symb... | train/atomic-layer-etching/simulation-usecase/5/fig_2 | atomic-layer-etching/simulation-usecase/5/fig_2 | molecular-structure-diagram | train | [
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Fig. 3 Snapshots of Ge surface after $100\mathrm{eV}$ Ar bombardment (200 times). Light green: Cl. Cyan: Ge. | train/atomic-layer-etching/simulation-usecase/5/fig_3 | atomic-layer-etching/simulation-usecase/5/fig_3 | molecular-structure-diagram | train | [
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Fig. 2. (a) Front and top views of the Si(111) - $(4\times 2)$ surface geometry, dark yellow atoms are Si-adatom and Si-restatom with a dangling bond, the red dotted lines are periodic boundary conditions (PBC). (b) The optimized geometry of chlorinated Si(111) surface, a $\mathrm{SiCl_2}$ is generated on the adato... | train/atomic-layer-etching/simulation-usecase/9/fig_2 | atomic-layer-etching/simulation-usecase/9/fig_2 | molecular-structure-diagram | train | [
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Fig. 4. Molecular structure of the selected cluster for TDDFT calculations. The cluster was extracted from the optimized slab (see Fig. 2(b)) and selected by convergence tests (see Fig. A2). | train/atomic-layer-etching/simulation-usecase/9/fig_4 | atomic-layer-etching/simulation-usecase/9/fig_4 | molecular-structure-diagram | train | [
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Fig. 5. HOMO and LOMO diagrams within the localized $\mathrm{SiCl_2}$ region, side view of Fig. 4 is selected for a better visualization. | train/atomic-layer-etching/simulation-usecase/9/fig_5 | atomic-layer-etching/simulation-usecase/9/fig_5 | molecular-structure-diagram | train | [
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Fig. 6. Hole and electron distributions related to the lowest excitation, $\mathrm{pink} =$ hole, blue $=$ electron, hole indicates the loss of electron. | train/atomic-layer-etching/simulation-usecase/9/fig_6 | atomic-layer-etching/simulation-usecase/9/fig_6 | molecular-structure-diagram | train | [
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