Novel electrochemical double layer capacitors with carbon nanotube (CNT) electrode, often referred to as supercapacitors, have a potential to bridge a power and energy gap between traditional dielectric capacitors and chemical batteries. However, their future is uncertain because current fabrication technologies involve difficult-to-control post-growth manipulations of CNTs. This paper addresses this problem by introducing model-based design of low-temperature CNT synthesis that is suitable for in-situ fabrication of CNT-based supercapacitor electrode. The insight to the surface kinetics during low-temperature CNT synthesis via catalytic oxidation was obtained via coupled Molecular Dynamics and Quantum Semiempirical Hamiltonian simulations. It was determined that the presence of oxygen on the surface of catalyst increases, by several times, the time necessary for the decomposition of hydrocarbons as well as shifts the reaction zone from the surface of catalyst to the catalyst underlayer. Theoretical trends were confirmed by CNT growth experiments. A contact between conducting CNTs and zinc oxide binding layer was analyzed in detail since its properties strongly affect the performance of CNT electrode. It was demonstrated that the formed CNT-zinc oxide interface was free from unbonded oxygen atoms and/or clusters of zinc atoms and was weakly affected by defects in CNTs.