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Supplementary information Figure S1 Schematic diagram depicting the SWCNT assembly process. 1,2-dichlorobenzene is used to prepare SWCNT suspensions. Methods: Substrate preparation. Polycrystalline Au films are prepared by thermally depositing 2nm thick Ti layer followed by 8nm Au layer on SiO2 substrates under a high vacuum condition (pressure ~ 2 x 10 -7 torr). We can routinely obtain lattice resolved AFM images on Au films prepared by this method. Surface functionalization. The surface functionalization and passivation of substrates are done by patterning first self-assembled monolayers on the substrate via direct deposition methods such as DPN or microcontact printing and backfilling the remaining area with a second molecular species. DPN utilizes an atomic force microscope (AFM) tip to deposit organic molecules onto solid substrates as a nanoscale “dip-pen.” The microcontact printing method relies on polymer stamps to create molecular patterns over large surface area. DPN and microcontact printing are done as described in the literature1–3. The backfilling step is done by immersing the substrate in the desired molecular solution (~3mM in ethanol) for 2 minutes. The CP AFM (Digital Instruments) equipped with a temperature controller, a humidity controller, a closed loop scanner, and the DPN software (NanoInk, Inc) is utilized for AFM topography imaging and DPN writing. LFM is also used to characterize molecular patterns. Highest grade SAM molecules and solvents are purchased from Aldrich and Fisher, respectively. To passivate the SiO2 surface, the substrate is placed in the octadecyltrichlorosilane solution in anhydrous hexane (1:1000 by volume) for 3 minutes. The detailed steps for SWCNT assembly on electrodes can be obtained from the authors. Carbon nanotube assembly. Purified SWCNTs (Carbon Nanotechnologies, Inc) are mixed with 1,2-dichlorobenzene and sonicated for 20 minutes to prepare a SWCNT suspension. Two typical concentrations for SWCNT suspensions in 1,2-dichlorobenzene are: 1) 0.2mg/ml and 2) 0.02mg/ml. To remove magnetic catalysis nanoparticle impurities from a SWCNT suspension, a small magnet (Digital Instruments) is placed near the suspension, and only the clean part of the suspension is extracted. For SWCNT assembly, the patterned surface is placed in the suspension usually for 10 seconds, and it is rinsed thoroughly with clean 1,2-dichlorobenzene. 1. Hong, S. & Mirkin, C. A. A nanoplotter with both parallel and serial writing capabilities. Science 288, 1808-1811 (2000). 2. Demers, L. M. et al. Direct patterning of modified oligonucleotides on metals and insulators by dip-pen nanolithography. Science 296, 1836-1838 (2002). 3. Xia, Y. & Whitesides, G. M. Use of controlled reactive spreading of liquid alkanethiol on the surface of gold to modify the size of features produced by microcontact printing. J. Am. Chem. Soc. 117, 3274-3275 (1995).