Atomistic simulations were performed with each of the prepared systems to gain an insight in the molecular level behavior of the nanosensor conjugate as it binds to the analyte molecules. The systems were described with CHARMM36 force field parameters as they have been successfully used to model interactions between ssDNA molecules and SWCNTs in previous studies. The parameters for the analyte compounds were generated from the CGenFF website, based on CHARMM36 general force field parameters. The simulations were performed with NAMD2.13 package 66 using Langevin dynamics in the NpT ensemble, where the value of the Langevin constant 𝛾 𝐿𝑎𝑛𝑔 was set at 1.0 ps -1 , the pressure remained constant at 1 bar, and the temperature remained constant at 298 K. The integration time step was set to 2 fs, and Coulomb and van der Waals non-bonded interactions were evaluated every one-and twotime steps, respectively, for all atoms within a 12 Å cutoff distance. The long-range Coulomb interactions were evaluated using the particle-mesh Ewald (PME) method, with periodic boundary conditions applied in all directions. After 5,000 steps of minimization, solvent molecules were equilibrated for 0.1 ns around the ssDNA-SWCNT conjugate. For this purpose, the atoms were restrained using harmonic forces with a spring constant of 1 kcal (mol•Å) -1 . Next, the systems were equilibrated in production MD runs, with harmonic wall restraints applied on the ssDNA side chains (A and C) and the small molecules. For the harmonic wall restraints, upper and lower walls were defined at 19 and -19 Å, respectively and a spring constant of 10 kcal (mol•Å) -1 was applied. The lengths of all simulations are listed in Table .