{"id":306614,"date":"2025-10-15T23:46:12","date_gmt":"2025-10-15T23:46:12","guid":{"rendered":"https:\/\/www.europesays.com\/us\/306614\/"},"modified":"2025-10-15T23:46:12","modified_gmt":"2025-10-15T23:46:12","slug":"patchy-nanoparticles-by-atomic-stencilling","status":"publish","type":"post","link":"https:\/\/www.europesays.com\/us\/306614\/","title":{"rendered":"Patchy nanoparticles by atomic stencilling"},"content":{"rendered":"<p>Chemicals<\/p>\n<p>All chemicals were used without further purification after purchase: gold(III) chloride trihydrate (\u226599.9% trace metals basis, HAuCl4\u00b73H2O, Sigma-Aldrich), sodium borohydride (99%, NaBH4, Sigma-Aldrich), sodium iodide (99.999%, NaI, Sigma-Aldrich), sodium bromide (\u226599.99%, NaBr, Sigma-Aldrich), sodium chloride (99.3%, NaCl, Fisher Scientific), potassium iodide (\u226599.5%, KI, Sigma-Aldrich), silver nitrate (\u226599.0%, AgNO3, Sigma-Aldrich), sodium tetrachloropalladate(II) (approximately 36%, Na2PdCl4, Acros Organics), l-ascorbic acid (BioXtra, \u226599.0%, AA, Sigma-Aldrich), sodium hydroxide (99.99%, NaOH, Sigma-Aldrich), cetyltrimethylammonium chloride (&gt;95%, CTAC, TCI, product number: H0082), benzyldimethylhexadecylammonium chloride (\u226597.0%, BDAC, Sigma-Aldrich), cetylpyridinium chloride (&gt;98.0%, CPC, TCI, product number: H0078), sodium citrate tribasic dihydrate (\u226599.0, C6H5Na3O7, Sigma-Aldrich), PS154-b-PAA51 (Mn\u2009=\u200916,000 for the PS block and Mn\u2009=\u20093,700 for the PAA block, Mw\/Mn\u2009=\u20091.04, Polymer Source Inc.), PS154-b-poly(acrylamide)49 (Mn\u2009=\u200916,000 for the PS block and Mn\u2009=\u20093,500 for the poly(acrylamide) block, Mw\/Mn\u2009=\u20091.15, Polymer Source Inc.), PS154-b-poly(ethylene oxide)170 (Mn\u2009=\u200916,000 for the PS block and Mn\u2009=\u20097,500 for the poly(acrylamide) block, Mw\/Mn\u2009=\u20091.09, Polymer Source Inc.), 2-NAT (99%, Sigma-Aldrich), biphenyl-4-thiol (97%, Sigma-Aldrich), DMF (anhydrous, 99.8%, Sigma-Aldrich) and hydrochloric acid (99.999% metals basis, HCl, Alfa Aesar). Nanopure deionized (DI) water (18.2\u2009M\u03a9\u2009cm at 25\u2009\u00b0C) purified by a Milli-Q Advantage A10 system was used. Note that the purity of cetyltrimethylammonium bromide (CTAB) is important for gold NP synthesis. We have used three types of CTAB: (1) Sigma-Aldrich, for molecular biology, \u226599%, product number: H6269; (2) Sigma-Aldrich, BioXtra, \u226599%, product number: H9151; and (3) Sigma-Aldrich, BioUltra, \u226599.0%, product number: 52365. For the data presented in this work, CTAB (1) and CTAB (2) were used for the experiments performed before February 2024. CTAB (3) has been used to reproduce the experiments afterwards.<\/p>\n<p>Synthesis of core NPs<\/p>\n<p>Gold octahedron, cuboctahedron, rhombic dodecahedron, cube and bipyramid NPs were synthesized following previously reported methods with slight modifications<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 33\" title=\"O&#x2019;Brien, M. N., Jones, M. R., Brown, K. A. &amp; Mirkin, C. A. Universal noble metal nanoparticle seeds realized through iterative reductive growth and oxidative dissolution reactions. J. Am. Chem. Soc. 136, 7603&#x2013;7606 (2014).\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#ref-CR33\" id=\"ref-link-section-d73953070e2899\" rel=\"nofollow noopener\" target=\"_blank\">33<\/a>,<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 34\" title=\"Lee, J.-H., Gibson, K. J., Chen, G. &amp; Weizmann, Y. Bipyramid-templated synthesis of monodisperse anisotropic gold nanocrystals. Nat. Commun. 6, 7571 (2015).\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#ref-CR34\" id=\"ref-link-section-d73953070e2902\" rel=\"nofollow noopener\" target=\"_blank\">34<\/a> (Supplementary Note\u00a0<a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">1<\/a>). Palladium cubes were synthesized following previous literature<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 51\" title=\"Chen, L. et al. Imaging the kinetics of anisotropic dissolution of bimetallic core&#x2013;shell nanocubes using graphene liquid cells. Nat. Commun. 11, 3041 (2020).\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#ref-CR51\" id=\"ref-link-section-d73953070e2909\" rel=\"nofollow noopener\" target=\"_blank\">51<\/a> with modifications (Supplementary Note\u00a0<a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">2.8<\/a>).<\/p>\n<p>Synthesis of patchy NPs<\/p>\n<p>Patchy NPs were synthesized in two steps, which are iodide masking and ligand-mediated polymer grafting. Using the patchy octahedra in Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"figure anchor\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#Fig3\" rel=\"nofollow noopener\" target=\"_blank\">3c<\/a> as an example, for the iodide-masking step, we first degas DI water by purging with N2 for 1\u2009h to minimize oxygen content. This degassed water is used throughout the masking step to minimize the oxidative etching of NPs. A gold octahedra solution was centrifuged at 2,400\u2009\u00d7\u2009g for 15\u2009min and the resulting pellet was diluted in 20\u2009mM CTAC with degassed water to achieve a final NP concentration of 0.5 optical density (OD) at a maximum extinction wavelength \u03bbmax (Stock Solution I). Next, 5.75\u2009\u00b5l of freshly prepared iodide solution (1\u2009ml of 10\u2009mM NaI, 500\u2009\u00b5l of 200\u2009mM NaOH and 8.5\u2009ml degassed DI water) was added dropwise to 6.9\u2009ml of Stock Solution I under mild vortex and incubated undisturbed for 30\u2009min. After the incubation, 2.1\u2009ml of 40\u2009mM CTAB was added, followed by three rounds of centrifugation (3,400\u2009\u00d7\u2009g, 5,300\u2009\u00d7\u2009g and 2,200\u2009\u00d7\u2009g for 15\u2009min each). The supernatant was removed after each centrifugation and a 10-\u00b5l pellet was redispersed in 10\u2009ml of 20\u2009mM CTAB after the first round and 1\u2009ml of DI water after the second round, respectively. The final pellet from the third centrifugation, after supernatant removal, was diluted with DI water to reach 5.0\u2009OD at \u03bbmax with 0.07\u2009mM CTAB (Stock Solution II). The final CTAB concentration can be varied depending on differently shaped NPs, as provided in Supplementary Note\u00a0<a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">2<\/a>.<\/p>\n<p>For ligand-mediated polymer grafting, still using the patchy octahedra in Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"figure anchor\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#Fig3\" rel=\"nofollow noopener\" target=\"_blank\">3c<\/a> as an example, we sequentially added 817\u2009\u00b5l DMF, 5\u2009\u00b5l of 2-NAT solution (2\u2009mg\u2009ml\u22121 in DMF), 200\u2009\u00b5l of Stock Solution II and 80\u2009\u00b5l of PS-b-PAA (8\u2009mg\u2009ml\u22121 in DMF) into an 8-ml vial under mild vortex. The vial was tightly capped with a Teflon-lined cap, sonicated for 5\u2009s, Parafilm-sealed and heated at 110\u2009\u00b0C in an oil bath for 2\u2009h without disturbance. After cooling to room temperature in the oil bath, the reaction mixture was transferred to a 1.5-ml microcentrifuge tube and centrifuged three times at 3,400\u2009\u00d7\u2009g, 1,300\u2009\u00d7\u2009g and 1,000\u2009\u00d7\u2009g (15\u2009min each) to remove molecular residues. After each centrifugation, 1.49\u2009ml of the supernatant was removed and a 10-\u00b5l pellet was redispersed in 1.49\u2009ml of water. Following the final centrifugation, the 10-\u00b5l pellet was diluted with 90\u2009\u00b5l of water for subsequent characterizations and self-assembly experiments. Detailed descriptions of the experimental procedure of the synthesis of other patchy NPs are provided in Supplementary Note\u00a0<a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">2<\/a> and Supplementary Tables <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">2<\/a>\u2013<a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">8<\/a>.<\/p>\n<p>Similar procedures with modifications can be extended to palladium nanocubes (Supplementary Note\u00a0<a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">2.8<\/a>), other thiols and block copolymers (Supplementary Notes\u00a0<a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">2.1<\/a> and <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">2.5<\/a>) and scale-up synthesis (Supplementary Note\u00a0<a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">2.9<\/a>).<\/p>\n<p>Large-scale self-assembly of patchy NPs<\/p>\n<p>For self-assembly experiments, a patchy NP solution in a 1.5-ml microcentrifuge tube was left undisturbed overnight, allowing the particles to sediment and concentrate (\u226530.0\u2009OD at \u03bbmax).<\/p>\n<p>Coffee ring effect-driven assembly on a silicon wafer<\/p>\n<p>A silicon wafer (3\u2009\u00d7\u20093\u2009mm2, Ted Pella) was cleaned with water, acetone and isopropanol through sonication for 5\u2009min each, followed by 60\u2009s of O2 plasma treatment using a Harrick Plasma PDC-32 (maximum RF power of 18\u2009W) to make the surface hydrophilic. Meanwhile, a 4\u2009\u00d7\u20094-inch2 piece of Parafilm was placed on a TechniCloth (TX609, Texwipe) with a water-filled Petri dish cover (60\u2009\u00d7\u200915\u2009mm2, Falcon) on top. 3.5\u2009\u00b5l of a concentrated patchy NP solution was drop-casted onto the wafer on the Parafilm. Immediately after drop-casting, both the silicon wafer and Petri dish were covered by a large Petri dish (100\u2009\u00d7\u200915\u2009mm2, VWR) and gently pressed down to seal against the Parafilm, maintaining a humid environment (humidity: 75\u201380%). A typical drying process takes 16\u201324\u2009h at room temperature (Supplementary Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">38a<\/a>).<\/p>\n<p>Capillary force-driven assembly in a glass capillary tube<\/p>\n<p>A 10-\u00b5l glass capillary tube (inner diameter: 0.5573\u2009mm, Drummond Scientific Company) was filled with 2\u2009M NaOH, incubated for 20\u2009min, rinsed with water and dried to make the inner wall hydrophilic before use. 5\u2009\u00b5l of concentrated patchy NP solution was then drawn into the capillary tube, keeping the NP solution several centimetres away from both tube ends. The capillary tube was suspended inside a loosely capped 15-ml centrifuge tube, which was then placed in a desiccator until the solution had fully dried, forming a visible gold ring around the interior. See the experimental set-up in Supplementary Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">38b<\/a>.<\/p>\n<p>Electron microscopy characterizationsTEM, SEM and STEM characterizations<\/p>\n<p>TEM images were acquired with a JEOL 2100 LaB6 transmission electron microscope operated at 200\u2009kV. SEM images were captured using an FEI Helios NanoLab 600i operated at 2\u2009kV with a beam current of 0.17\u2009nA and a working distance of 4.0\u2009mm. HAADF-scanning transmission electron microscopy (STEM) imaging was conducted on a probe aberration-corrected Thermo Fisher Scientific Themis Z scanning transmission electron microscope operated at 300\u2009kV. STEM-EDX mapping was acquired with a Thermo Fisher Scientific \u2018Kraken\u2019 Spectra 300 operated at 60\u2009kV equipped with Dual-X EDX detectors with a collection angle of 1.76\u2009sr.<\/p>\n<p>Sample preparation for HAADF-STEM characterization<\/p>\n<p>For NP facet imaging and analysis, solutions of pristine NPs were drop-casted on TEM grids, with CTAB concentration reduced through three rounds of centrifugation. Approximately 50\u2013200\u2009\u00b5l of the pristine NP solutions in 40\u2009mM CTAB was used per sample. Each sample was first diluted with 1\u2009ml of water in 1.5-ml microcentrifuge tubes, followed by removing 990\u2009\u00b5l of supernatant after each of the first two centrifugations. After each centrifugation, a 10-\u00b5l pellet was redispersed in 990\u2009\u00b5l of water. Following the third centrifugation, a 1.5-\u00b5l pellet was drop-casted onto a carbon-coated copper TEM grid (Electron Microscopy Sciences, CF400-Cu) and dried completely. Before imaging, samples were plasma-cleaned for 2\u2009min at 15\u2009W under a 12-sccm flow of Ar\u2009+\u2009O2 to remove residual CTAB molecules covering NPs using a PIE Scientific Tergeo-EM plasma cleaner.<\/p>\n<p>HAADF-STEM imaging<\/p>\n<p>HAADF images were acquired with a beam current of approximately 20\u2009pA and semi-convergence angle of 18\u2009mrad. The camera length was 115\u2009mm and the collection angles of the HAADF detector were 62\u2013200\u2009mrad for image acquisition. To minimize image distortion from sample drift, several sequential frames (10\u201350\u2009frames) with short dwell time (100\u2013500\u2009ns) were acquired, which were used to render drift-corrected frames to enhance the contrast.<\/p>\n<p>TEM tomography<\/p>\n<p>TEM images for tomography reconstruction were collected by titling the samples from 0\u00b0 to \u221260\u00b0 and then from 0\u00b0 to +60\u00b0 in 2\u00b0 intervals, capturing 61 images per sample. To minimize beam damage, a low electron dose rate of 6\u20138\u2009e\u2212\u2009\u00c5\u22122\u2009s\u22121 was used. To improve the polymer patch contrast, a defocus of \u22122,048\u2009nm was used. Image alignment and contrast-transfer function correction were performed using IMOD64 4.9.3 software<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 52\" title=\"Kremer, J. R., Mastronarde, D. N. &amp; McIntosh, J. R. Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 116, 71&#x2013;76 (1996).\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#ref-CR52\" id=\"ref-link-section-d73953070e3091\" rel=\"nofollow noopener\" target=\"_blank\">52<\/a>. Tomograms were generated using OpenMBIR with diffuseness of 0.3 and smoothness of 0.2 as reconstruction parameters, which uses a model-based iterative algorithm of tomogram reconstruction<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 53\" title=\"Yan, R., Venkatakrishnan, S. V., Liu, J., Bouman, C. A. &amp; Jiang, W. MBIR: a cryo-ET 3D reconstruction method that effectively minimizes missing wedge artifacts and restores missing information. J. Struct. Biol. 206, 183&#x2013;192 (2019).\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#ref-CR53\" id=\"ref-link-section-d73953070e3095\" rel=\"nofollow noopener\" target=\"_blank\">53<\/a>. 3D models of the tomograms were visualized using Amira 6.4 from Thermo Fisher Scientific. The tomograms were denoised using three filters: median (3\u2009\u00d7\u20093\u2009\u00d7\u20093 voxel neighbourhood, iterations 26), Gaussian filter (kernel size 9, 3\u2009\u00d7\u20093\u2009\u00d7\u20093 standard deviation) and edge-preserving smoothing (time 25, step 5, contrast 3.5 and sigma 3). Polymer patches and gold NPs were segmented by greyscale intensity thresholding and refined manually in Amira 6.4 software.<\/p>\n<p>STEM-EDX characterization<\/p>\n<p>Samples for the STEM-EDX analysis were prepared by drop-casting Stock Solution II on carbon-coated copper TEM grids (Electron Microscopy Sciences, CF400-Cu). The octahedra and cuboctahedra were iodide-masked. To minimize carbon contamination, the TEM grids were baked overnight at 130\u2009\u00b0C in high vacuum to remove excess CTAB. STEM-EDX maps were acquired with a 120-pA probe current, a 30-mrad semi-convergence angle and continuous raster-scanning with drift correction, using a 2-\u00b5s dwell time over approximately 4\u2009h. For iodide-masked cuboctahedra, the NPs were predominantly oriented on the carbon support along the [001] direction. Therefore, the stage was tilted 45\u00b0 to the [110] zone axis, aligning both the {111} and {100} facets \u2018edge-on\u2019. Elemental mapping was achieved by fitting and quantifying the peak intensities above the background using the Cliff\u2013Lorimer method<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 54\" title=\"Cliff, G. &amp; Lorimer, G. W. The quantitative analysis of thin specimens. J. Microsc. 103, 203&#x2013;207 (1975).\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#ref-CR54\" id=\"ref-link-section-d73953070e3108\" rel=\"nofollow noopener\" target=\"_blank\">54<\/a>. Two high-quality EDX maps of seven cuboctahedra were selected and a total of 1,692 line profiles were obtained (Supplementary Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">25<\/a>). Similarly, iodide-masked octahedra were oriented on the carbon support along the [110] direction and their \u2018edge-on\u2019 {111} facets were used for iodide concentration analysis (Extended Data Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"figure anchor\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#Fig7\" rel=\"nofollow noopener\" target=\"_blank\">2<\/a>).<\/p>\n<p>TEM image analysisPatch local thickness t<br \/>\n                              loc<\/p>\n<p>The tloc of patches was determined as the diameter of the largest circle that can fit within the patch and includes the target pixel. Patch contours were manually outlined in ImageJ to define the patch regions. The tloc map was then obtained using the built-in \u2018Local Thickness\u2019 function in ImageJ, as also detailed in our previous work<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 24\" title=\"Kim, A. et al. Symmetry-breaking in patch formation on triangular gold nanoparticles by asymmetric polymer grafting. Nat. Commun. 13, 6774 (2022).\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#ref-CR24\" id=\"ref-link-section-d73953070e3145\" rel=\"nofollow noopener\" target=\"_blank\">24<\/a>.<\/p>\n<p>Maximum patch thickness t<br \/>\n                              m and patch coverage fraction f<br \/>\n                              cov<\/p>\n<p>The values of tm and fcov were measured using a neural-network-based method on TEM images<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 55\" title=\"Yao, L. et al. Seeking regularity from irregularity: unveiling the synthesis&#x2013;nanomorphology relationships of heterogeneous nanomaterials using unsupervised machine learning. Nanoscale 14, 16479&#x2013;16489 (2022).\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#ref-CR55\" id=\"ref-link-section-d73953070e3176\" rel=\"nofollow noopener\" target=\"_blank\">55<\/a>. The neural network-based TEM image segmentation is detailed in Supplementary Note\u00a0<a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">3<\/a> and Supplementary Figs. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">32<\/a> and <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">33<\/a>. After training the neural network with manually labelled TEM images of diverse patchy NP shapes, a shape fingerprint t was extracted from the patch contours. First, the centroid of the gold NP was identified and rays extending from \u03b8\u2009=\u2009\u2212180\u00b0 to \u03b8\u2009=\u2009179\u00b0 at 1\u00b0 intervals were drawn from the centroid. The distance that each ray travels within the patch region was recorded as a function of \u03b8. tm is determined by the maximum value of t and fcov is identified as the range of \u03b8 in which t is non-zero. See detailed description in Supplementary Note\u00a0<a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">3<\/a> and Supplementary Figs. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">34<\/a>\u2013<a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">36<\/a>.<\/p>\n<p>Other characterizationsUV\u2013Vis measurements<\/p>\n<p>Ultraviolet\u2013visible (UV\u2013Vis) spectra were measured using a Scinco S-4100 PDA spectrophotometer with a quartz cuvette (path length\u2009=\u20091\u2009cm, VWR).<\/p>\n<p>XPS characterization<\/p>\n<p>XPS analysis was performed using a Kratos Axis Ultra equipped with a monochromatic Al K\u03b1 radiation X-ray source and an energy resolution of 0.4\u2009eV. Before characterization, 10\u2009\u00b5l of each Stock Solution II, prepared with various iodide concentrations, was drop-casted on a silicon wafer cleaned with water, acetone and isopropanol and then fully dried. The silicon wafers were fixed to the sample bar and transported to the instrument in an airtight container under an Ar atmosphere for XPS signal acquisition. Data processing and peak fitting were conducted using the CasaXPS software. Atomic concentrations within samples were calculated by integrating the fitted XPS spectra for all analysed regions and adjusting for atomic relative sensitivity factors. See detailed sample conditions in Supplementary Table <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">9<\/a>.<\/p>\n<p>Raman characterization<\/p>\n<p>Raman characterization was performed using a Horiba XploRA-nano TERS\/TEPL with a 100\u00d7 objective lens. The Raman samples were prepared following two steps, without polymer grafting (Supplementary Table <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">10<\/a>). First, gold octahedra were iodide-masked in varying [I\u2212] and then concentrated to reach 20.0\u2009OD at \u03bbmax in 0.07\u2009mM CTAB, following the iodide-masking procedure described above. Next, 40\u2009\u00b5l of 2-NAT (0.2\u2009mg\u2009ml\u22121 in DMF) and 200\u2009\u00b5l of the iodide-masked octahedra were sequentially added into 860\u2009\u00b5l of DMF in a vial with mild vortex. The remaining reaction condition and washing steps follow the standard iodide masking procedure, except for centrifugation, which was performed three times at 2,900\u2009\u00d7\u2009g for 15\u2009min and 2,400\u2009\u00d7\u2009g for 7\u2009min twice. After the first two centrifugations, the pellet was resuspended in 1\u2009ml of DMF. After the final centrifugation, the sediment was redispersed in 20\u2009\u00b5l of DMF and the NP concentration was adjusted to 13.0\u2009OD at \u03bbmax by adding water. A 5-\u00b5l aliquot of this NP solution was drop-casted onto a clean glass slide. The glass slide was used after washing with isopropyl alcohol and water and then fully dried. Raman measurements were performed with a 638-nm excitation wavelength, 1-mW laser power and three scans for average (90\u2009s exposure time each).<\/p>\n<p>X-ray tomography of large-scale self-assembly<\/p>\n<p>The X-ray tomography sample was prepared through a focused-ion beam milling using the FEI Helios NanoLab 600i. Before milling, platinum was deposited on the self-assembled patchy rhombic dodecahedra on a silicon wafer, with a deposition diameter of 3\u2009\u00b5m and a thickness of 300\u2009nm. Subsequently, the assembly was milled into a cylinder with a diameter of 2.5\u2009\u00b5m. The shaped cylinder was lifted with an OmniProbe and mounted onto a tungsten needle tip (Supplementary Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">50<\/a>).<\/p>\n<p>X-ray tomography data were acquired at the hard X-ray nanoprobe beamline of National Synchrotron Light Source II at Brookhaven National Laboratory. A monochromatic beam at 12\u2009keV was selected and then focused by a set of crossed multilayer Laue lenses to produce a nanobeam<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 56\" title=\"Yan, H. et al. Hard X-ray nanoprobe: a scanning hard X-ray microscopy beamline offering multi-modal imaging capabilities at 10 nm. In X-ray Nanoimaging: Instruments and Methods IV 1111202 (SPIE, 2019).\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#ref-CR56\" id=\"ref-link-section-d73953070e3300\" rel=\"nofollow noopener\" target=\"_blank\">56<\/a> with a size of approximately 13\u2009nm. 2D fly-scans were performed in a grid pattern with at least 150\u2009\u00d7\u2009150\u2009pixels, 50-ms dwell time and 10-nm step size at every 2\u00b0 to collect 91 projections covering 180\u00b0. Far-field diffraction patterns were analysed with a ptychographic reconstruction algorithm to retrieve both the complex-valued probe and the object functions. The acquired fluorescence spectra were fitted using the software package PyXRF. Individual 2D frames were coarsely aligned using ImageJ 1.5, MultiStackReg plugin, whereas fine alignments were adjusted with a cross-correlation function in Tomviz 1.9, followed by 3D reconstruction. The data were further processed by Fourier filtering using the sharp lattice peaks in the reciprocal space image of the superlattice to remove noise and sharpen the particle positions for subsequent segmentation, using Dragonfly 2020.2 software<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 57\" title=\"Michelson, A. et al. Three-dimensional visualization of nanoparticle lattices and multimaterial frameworks. Science 376, 203&#x2013;207 (2022).\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#ref-CR57\" id=\"ref-link-section-d73953070e3304\" rel=\"nofollow noopener\" target=\"_blank\">57<\/a>.<\/p>\n<p>DFT calculations of gold surfaces with iodide and 2-NAT<\/p>\n<p>All DFT calculations were performed using the Vienna Ab initio Simulation Package<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" title=\"Kresse, G. &amp; Hafner, J. Ab initio molecular dynamics for liquid metals. Phys. Rev. B 47, 558&#x2013;561 (1993).\" href=\"#ref-CR58\" id=\"ref-link-section-d73953070e3317\">58<\/a>,<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" title=\"Kresse, G. &amp; Furthm&#xFC;ller, J. Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set. Phys. Rev. B 54, 11169&#x2013;11186 (1996).\" href=\"#ref-CR59\" id=\"ref-link-section-d73953070e3317_1\">59<\/a>,<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 60\" title=\"Kresse, G. &amp; Hafner, J. Ab initio molecular-dynamics simulation of the liquid-metal&#x2013;amorphous-semiconductor transition in germanium. Phys. Rev. B 49, 14251&#x2013;14269 (1994).\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#ref-CR60\" id=\"ref-link-section-d73953070e3320\" rel=\"nofollow noopener\" target=\"_blank\">60<\/a> with projector augmented waves<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 61\" title=\"Bl&#xF6;chl, P. E. Projector augmented-wave method. Phys. Rev. B 50, 17953&#x2013;17979 (1994).\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#ref-CR61\" id=\"ref-link-section-d73953070e3324\" rel=\"nofollow noopener\" target=\"_blank\">61<\/a>. The generalized gradient approximation by Perdew, Burke and Ernzerhof was used for the exchange-correlation functional<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 62\" title=\"Perdew, J. P., Burke, K. &amp; Ernzerhof, M. Generalized gradient approximation made simple. Phys. Rev. Lett. 77, 3865&#x2013;3868 (1996).\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#ref-CR62\" id=\"ref-link-section-d73953070e3328\" rel=\"nofollow noopener\" target=\"_blank\">62<\/a>. We chose an energy cut-off of 450\u2009eV as an optimal value for our plane-wave basis set. For the sampling of the first Brillouin zone, Monkhorst\u2013Pack grids were used<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 63\" title=\"Monkhorst, H. J. &amp; Pack, J. D. Special points for Brillouin-zone integrations. Phys. Rev. B 13, 5188&#x2013;5192 (1976).\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#ref-CR63\" id=\"ref-link-section-d73953070e3332\" rel=\"nofollow noopener\" target=\"_blank\">63<\/a>. We also included the DFT-D3 method of Grimme et al. with the Becke\u2013Johnson damping to describe long-range van der Waals interactions<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 64\" title=\"Grimme, S., Ehrlich, S. &amp; Goerigk, L. Effect of the damping function in dispersion corrected density functional theory. J. Comput. Chem. 32, 1456&#x2013;1465 (2011).\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#ref-CR64\" id=\"ref-link-section-d73953070e3336\" rel=\"nofollow noopener\" target=\"_blank\">64<\/a>. See details in Supplementary Note\u00a0<a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">4<\/a>.<\/p>\n<p>Computation and theory modelling of patchy NPs and their assembliesPatchy NP grafting simulation<\/p>\n<p>A library of individual patchy NPs was simulated using MD using the HOOMD-blue simulation engine<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 65\" title=\"Anderson, J. A., Glaser, J. &amp; Glotzer, S. C. HOOMD-blue: a Python package for high-performance molecular dynamics and hard particle Monte Carlo simulations. Comput. Mater. Sci. 173, 109363 (2020).\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#ref-CR65\" id=\"ref-link-section-d73953070e3356\" rel=\"nofollow noopener\" target=\"_blank\">65<\/a>. First, a single anisotropic particle was placed at the centre of the simulation box. Polymer chains with one grafting end were then randomly distributed on the surface of the central anisotropic particle and allowed to freely move on the surface to find their equilibrium positions. The location of iodide-masked regions predicted from our iodide adsorption theory (see details in Supplementary Note\u00a0<a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">5<\/a>) were modelled as spherical beads that are strongly repulsive to the polymer chains. All chain\u2013chain interactions exhibit Lennard\u2013Jones attraction with each other to capture the PS\u2013PS aggregation in experimental conditions. All other interactions were purely repulsive and modelled using the Weeks\u2013Chandler\u2013Andersen repulsive potential. For detailed description, see Supplementary Note\u00a0<a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">8<\/a>.<\/p>\n<p>Theoretical prediction of patches<\/p>\n<p>Polymer patch patterns and sizes were theoretically predicted using MC grafting simulation involving two steps: (1) determining the surface distribution of iodide-masked region and (2) placing polymer chains onto the unmasked (\u2018free\u2019) surface sites, while accounting for chain\u2013chain interactions. We began by constructing a grid of points on the core NP surface, defining potential sites for iodide or polymer attachment. Using the Metropolis algorithm with surface energies computed from DFT, iodide-masked points were placed on the various surface sites (Supplementary Note\u00a0<a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">5<\/a>). Placing iodide-masked points on the particle surface uses the Metropolis algorithm, guided by surface energies computed from DFT. Iodide-masked points cannot accommodate polymer grafting, leaving the remaining open locations as the only \u2018free\u2019 sites for polymer grafting. After an occupancy matrix logs iodide-masked positions, the first polymer chain grafts on the surface based on its Boltzmann-weighted free energy as a function of surface locations. The matrix updates with this chain attachment and \u2018free\u2019 surface sites within a correlation length \u03be of any polymer-occupied sites gain a favourable chain\u2013chain interaction, governed by the Flory\u2013Huggins parameter \u03c7 (Supplementary Note\u00a0<a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">6<\/a>). This entire process repeats for each polymer chain until the target grafting density is achieved. See Supplementary Note\u00a0<a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">7<\/a> for details.<\/p>\n<p>Simulation of patchy NP self-assembly<\/p>\n<p>MC simulations were performed to obtain the self-assemblies of patchy NPs, using the HOOMD-blue simulation engine<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 65\" title=\"Anderson, J. A., Glaser, J. &amp; Glotzer, S. C. HOOMD-blue: a Python package for high-performance molecular dynamics and hard particle Monte Carlo simulations. Comput. Mater. Sci. 173, 109363 (2020).\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#ref-CR65\" id=\"ref-link-section-d73953070e3397\" rel=\"nofollow noopener\" target=\"_blank\">65<\/a>. We first defined a patchy particle whose patch locations and sizes are commensurate with those measured from the above MD simulation and validated with theory and experiments. Patches were modelled to exhibit hard sphere interactions with each other to capture the strong PAA\u2013PAA electrostatic repulsions between the outer surface of the patches (Supplementary Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">49<\/a>). The core NP interactions were modelled using a Kern\u2013Frenkel attraction between the various surface sites that were not covered by polymeric patches. See Supplementary Note\u00a0<a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41586-025-09605-8#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">9<\/a> for details.<\/p>\n","protected":false},"excerpt":{"rendered":"Chemicals All chemicals were used without further purification after purchase: gold(III) chloride trihydrate (\u226599.9% trace metals basis, HAuCl4\u00b73H2O,&hellip;\n","protected":false},"author":3,"featured_media":306615,"comment_status":"","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[8],"tags":[10046,10047,102407,159,61524,67,132,68],"class_list":{"0":"post-306614","1":"post","2":"type-post","3":"status-publish","4":"format-standard","5":"has-post-thumbnail","7":"category-science","8":"tag-humanities-and-social-sciences","9":"tag-multidisciplinary","10":"tag-nanoparticles","11":"tag-science","12":"tag-self-assembly","13":"tag-united-states","14":"tag-unitedstates","15":"tag-us"},"share_on_mastodon":{"url":"https:\/\/pubeurope.com\/@us\/115380852192672527","error":""},"_links":{"self":[{"href":"https:\/\/www.europesays.com\/us\/wp-json\/wp\/v2\/posts\/306614","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.europesays.com\/us\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.europesays.com\/us\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/us\/wp-json\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/us\/wp-json\/wp\/v2\/comments?post=306614"}],"version-history":[{"count":0,"href":"https:\/\/www.europesays.com\/us\/wp-json\/wp\/v2\/posts\/306614\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/us\/wp-json\/wp\/v2\/media\/306615"}],"wp:attachment":[{"href":"https:\/\/www.europesays.com\/us\/wp-json\/wp\/v2\/media?parent=306614"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.europesays.com\/us\/wp-json\/wp\/v2\/categories?post=306614"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.europesays.com\/us\/wp-json\/wp\/v2\/tags?post=306614"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}