Self-assembly of carbon nanotubes (CNTs) on silicon substrates has myriad applications including nanotube based electrochemical energy conversion and storage devices, such as batteries and super-capacitors. Patterned assembly of CNTs is required in order to control the effective electrical conductivity and mechanical properties of these devices and achieve substantial improvement in their performance. Solution-based self-assembly of CNTs provides a cost-effective means to synthesize uniform vertically or horizontally aligned nanostructures on top of substrates. However, self-assembly of CNTs is a complex dynamical process that involves intermolecular interaction between the CNTs and that between the nanotubes and the substrate as well as solvent molecules. The transport properties of CNTs and solvents also play an important role. The scientific literature lacks detailed study of understanding the mechanism of self-assembly of CNTs on substrates during synthesis process. Often times, nanotubes are functionalized in an effort to make them more soluble and induce partial charges to control the self-assembly. Some of the key factors that govern the transportation and self-assembly of functionalized CNTs are surface charge density on substrate and electrostatic interaction of the functionalized CNTs with the substrate. In an effort to mimic the conditions during the synthesis of carbon nanomaterials on silicon substrate, we have employed molecular dynamics simulations to simulate both pure and functionalized CNTs sandwiched between silicon substrates in presence of commonly used solvent, water. Our simulations indicate that both pure and functionalized CNTs are not significantly soluble in water and form agglomerates. Our results also illustrate that neither pure nor functionalized CNTs tend to deposit on silicon substrates in water. Results presented in this study provide fundamental insight that can help to understand the agglomeration and orientation of CNTs in water.

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