As a first step, we built an atomistic model of Ih 309 (Figure ) that we simulated via 2 µs of MD at 300 K (see Methods section for complete computational details). From the resulting MD trajectories, we extracted 1000 frames sampled every 1 ns from the last 1 µs of MD (during which the population of the detected AEs plateau -MD steady state -see Supplementary Figure ). Recently proven useful to reconstruct the structural and dynamical complexity of various types of self-organizing molecular/atomic systems, we used the smooth overlap of atomic positions (SOAP) vectors as abstract high-dimensional descriptors capable of retaining rich information on order/disorder in the AEs -i.e., in the local atoms' displacement (Figure : in yellow) around each atom in the NP (in blue) within a cutoff. In particular, our SOAP analysis is performed using a cutoff of rcut = 4.48 Å, which was found as the best compromise between the cost of the calculation and the highest retained information in this case. At each sampled frame (1000) during the MD simulation, we calculated the SOAP power spectrum for each atom (309) in the Ih 309 NP, obtaining a global SOAP dataset composed of 309'000 SOAP spectra in total. From this SOAP dataset, we then identified the main AEs that populate the Ih 309 NP at 300 K via unsupervised clustering using the HDBSCAN* algorithm (see Methods section for complete details). This analysis finds 8 different clusters (AEs) emerging in the Ih 309 at 300 K (Figure ). Particularly evident in Figure , the identified SOAP clusters correspond to different structural AEs on the Ih 309 NP. In detail (Figure ), we obtain an "Ico" AE, corresponding to the central atom of the icosahedral Ih 309 NP (in blue). Shown in Figure , such AE is different from the "Bulk" AEs (in violet) surrounding it in the bulk of the NP (this 13 atoms AE is non-crystalline, i.e. it is not possible to cover the whole space by units of this AE). The analysis detects "SubSurf " and "5foldedSS" AEs, identifying the atoms in the first layer below the NP surface (deep blue) and vertexes (characterized by a 5-folded symmetry axis: in light blue). On the surface of the (ideal) Ih 309 NP (Figure ), our analysis detects a "Faces" (dark green) -close compact FCC(111) facet environments -, "Edges" (light green) and "Vertexes" AEs (the lowest coordinated atoms in the NP, in yellow). Shown in Figure , the analysis also detects an additional pink cluster, namely, a "Concave" AE identifying the centers of the so-called rosettes (Figure ). Noteworthy, such concave AEs are not present in the ideal Ih 309 NP (Figure ) but they emerge along the MD (see also Supplementary Movie 1), while their formation is known to be an energetically favored event on the surface of icosahedral NPs. . Figure shows a representative MD snapshot of the Ih 309 at 300 K, where a rosette triplet -formation of rosettes pertaining to three neighbor vertexes, known experimentally -is clearly visible. (notably, each rosette center (pink) has six atom neighbors while classic vertexes (yellow) have five in a Ih 309 NP). In particular, once a rosette triplet is formed, Figure . Bottom-up machine learning of atomic environments (AEs) and AEs' dynamics in Ih 309 at 300 K. (a) A SOAP vector is centered in each atom of the Au NP (in blue), obtaining a SOAP spectrum which is a characteristic fingerprint of the level of order/disorder in the displacement of the neighbor Au atoms (in gold) within a cutoff (shown as a transparent sphere). The SOAP spectra of all atoms in the NP (309) are calculated on 1000 frames taken every 1 ns along the last 1 µs of MD (see also Supplementary Figure ), obtaining a SOAP dataset containing 309'000 SOAP spectra in total. The main AEs that populate the Ih 309 NP are identified via unsupervised clustering using the HDBSCAN* algorithm (see Methods section for details). this configuration is found stable during the MD simulation, while even at 300 K, this is accompanied by continuous collective atoms motions that do not change the overall shape of the surface of the icosahedral NP (see Supplementary Movie 1).