## 2 Experimental Section  
Co NP samples were prepared by implanting Co ions at either liquid-N\({}_{2}\) temperature or 400 \({}^{\circ}\mathrm{C}\) into 2 \(\mu\)m thick SiO\({}_{2}\) layers thermally grown on Si (100) substrates. Implantation energies ranged from 416-1,400 keV with fluences varying from 3.8 \(\times\) 10\({}^{15}\) to 3.0 \(\times\) 10\({}^{17}\) /cm\({}^{2}\). The resulting peak Co concentrations ranged from 0.3 to 9.0 at.% as calculated by TRIM [33]. Samples were then annealed at 800-1,100 \({}^{\circ}\mathrm{C}\) under forming gas (5% H\({}_{2}\) + 95% N\({}_{2}\)) for 1 h to promote Co precipitation and NP growth. Selected samples were then irradiated at room temperature with \({}^{197}\)Au ions at energies of 9, 27, 54, 89, 110 and 185 MeV, where the ion penetration depth was beyond that of the NP distribution. The range, \(S_{e}\) and \(S_{n}\) for Au ions in a-SiO\({}_{2}\) and Co, as calculated by TRIM [33], are listed in Table 1.  
The NP shape and size were quantified with XTEM and SAXS, respectively. XTEM samples were prepared entirely at or below room temperature to stem thermal effects. Electron transparency was achieved with conventional mechanical thinning, polishing, and dimpling followed by ion milling at liquid-N\({}_{2}\) temperature with 3.5 keV Ar ions at an incident angle of 4\({}^{\circ}\). XTEM bright-field images and electron diffraction (ED) patterns were acquired using a Phillips CM300 microscope operating at 300 kV. For the synchrotron measurements, two unique sample preparation methods [34,35] were used to isolate the thin SiO\({}_{2}\) layer containing the Co NPs. For XAS samples, the Si substrate was initially removed through mechanical grinding and selective wet chemical etching with KOH, and then multiple NP rich SiO\({}_{2}\) layers were stacked together between two Kapton windows. As a consequence, considerable NP material was concentrated within the sample holder, scattering from the Si substrate was eliminated, and high-resolution measurements were enabled. For the SAXS measurements the thick Si substrate was thinned by mechanically grinding to a thickness of \(\sim\)200 \(\mu\)m. A concavity of \(\sim\)150 \(\mu\)m in depth was then formed in the Si substrate using a dimple grinder. The sample was finally placed in a KOH solution, and etched until a \(\sim\)1 mm window in the SiO\({}_{2}\) was formed. This sample preparation methodology results in a self-supporting and substrate-free NP rich thin SiO\({}_{2}\) layer for fast, high-contrast transmission SAXS measurements. Bulk Co XAS standards were prepared by thermal evaporation of a Co film 250 nm onto a SiO\({}_{2}\)/Si wafer followed by the plasma-enhanced chemical vapor deposition of a SiO\({}_{2}\) capping layer. To produce HCP material, samples were annealed at 400 \({}^{\circ}\)C in N\({}_{2}\) to remove disorder and any residual FCC component. FCC material was prepared by rapid thermal annealing at 900 \({}^{\circ}\)C in N\({}_{2}\) followed by rapid quenching. The purity of each phase was confirmed with x-ray diffraction. Fluorescence-mode XANES and EXAFS measurements were performed at beamline 20-B of the Photon Factory, Japan. Samples were measured at the Co \(K\)-edge (7.709 keV) between temperatures of 15 and 300 K. Spectra were recorded using a 6 \(\times\) 6 pixel-array Ge detector with the Si (111) monochromator detuned by 50% for harmonic rejection. Data were collected to a photoelectron wavenumber (\(k\)) value of 17 A\({}^{-1}\). For energy calibration, a Co HCP reference foil was simultaneously measured in transmission mode. Background subtraction, spectra alignment and normalization of the EXAFS data were performed with ATHENA [36]. The position of the Co \(K\)-edge was determined from the maximum of the first derivative of the absorption spectra.