Calculating Deflection of Micro-Cantilever with Self-Assembled Monolayer Molecules Using Molecular Dynamics Simulations
H-C Kan, Y-T Wang and S-H Tsai
National Center for High-performance Computing, TW
molecular dynamics simulations, CHARMM, self-assembled monolayer, SAM, Stoney equation, Dupré relation
Self-assembled Monolayers (SAM) by spontaneous adsorption of molecules on microscale substrates have attracted a huge interest due to their scientific importance and potential uses in technological applications and health care industry. Diverse selections of SAM in accompanying with various bio-molecules to form biological probes on the substrate surface have made the micro-cantilever an excellent device for studies of interactions between artificial surfaces and biological systems. By evaluating the change of Gibbs free energy of the adsorbed molecules, the deflection of the probe can be calculated, mechanically and thermodynamically, by the Stoney’s equation in associated with the Dupré relation. All computations of the free energy changes were performed isothermally with periodic boundary conditions (PBC) by commercial molecular dynamics (MD) simulation software CHARMM in associated with the specific molecular topology and force fields for alkanethiolic molecules (HS)(CH2)7CH3. The alkanethiolic molecules are arranged respectively in squared 4_4 and 8_8 array formats adsorbed on the Au atoms coated on the surface of the micro-cantilever. The effects of the seeding density of the adsorbed molecules are taken into consideration by different separations between Au atoms.
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Nanotech 2005 Conference Program Abstract