In silico studies of the interaction of the colon cancer receptor and RNA aptamer adsorbed on (1 0 1) facet of TiO2 nanoparticle investigated by molecular dynamics simulation

Improved delivery and competitive adsorption of paclitaxel and mitomycin C anticancer drugs on boron nitride nanoparticles: a molecular dynamics insight

“…S3(c) (ESI†) show good flexibility of adsorbed PX ligands onto BNNSs along 50 ns trajectories in the system containing PX ligands on the BNNS surface. As it has been previously reported in the literature, 78 Fig. S3(d) (ESI†) presents the MMC ligands RMSD during 50 ns simulation time of adsorption.…”

“…The performed protocol of simulation for all systems was containing “minimization, annealing, and a final 50 ns and 100 ns NPT (isothermal–isobaric) ensemble production simulation”. 77,78 During the NPT production simulation, temperature and pressure were considered to be fixed using a Langevin thermostat 79 and barostat. 80 In the NPT production run, the Langevin piston target was set to 1 atm.…”

“…For a better comparison of competitive aggregation, we used the MMC systems in TIP3P water solvent and aggregated adsorbed ones investigated in our previous published study. 78 The size of the PX-MMC-BNNS complex was (55.50 Å × 108.20 Å × 32.20 Å) and a 100 ns MD simulation in NPT ensemble has been done on this complex. Along the MD trajectories, the nanosheet atoms were considered fixed.…”