Molecular Dynamics Simulation of Conformational Transition and Frictional Performance Modulation of Densely Packed Self-Assembled Monolayers Based on Electrostatic Stimulation

Abstract

Self-assembled monolayers (SAMs) terminated with functional end groups such as polyethylene glycols (PEG) have attracted considerable attention because of their unique and flexible structure that exhibits conformational transition under electrostatic stimulation. Molecular dynamics simulations are used to investigate the conformational transition and associated modulation of frictional performance of densely packed PEG-terminated SAMs subjected to electrical field stimulation. Previously reported empirical potentials and atomic charges were used to model the intrachain bonds and electrostatic and interchain interactions. Simulation results indicate that significant conformational transition is generated because of the electrostatic forces. Under positive electrical fields, PEG groups are compressed and twisted into the helical form, "gauche" state, whereas under negative electrical fields, PEG groups are stretched into the straight form, "all-trans" state. Such conformational transition may lead to substantial alteration of frictional response upon SAMs. By shallow penetration and sliding using a repulsive indenter, the SAMs under positive electrical fields exhibit a level of frictional response that is comparatively lower than those under zero and negative potentials, which may be attributed to reduced interchain space for deformation, limited conformational transition, and less energy absorption. The simulation results demonstrate that with appropriate selection of functional end groups attached to SAM backbone chains it is possible to modulate frictional performance of densely packed SAMs via electrostatic stimuli.

Micro-cantilever based biosensor for electrical actuation and detecting molecular interactions

“…The conformational changes can affect the specific binding between aptamer and its complementary thrombin. This phenomenon has been observed in previous research using in-situ electrochemical atomic force microscopy (ECAFM) based DFS experiment (Ma and Shrotriya 2015).…”

“…With the same protocol as experiment 1, The sensing cantilever and reference cantilever were the same as the sensing and reference cantilevers in experiment 1, that is, incubating a cleaned bare gold cantilever in a solution containing 0.5 μM 5' thiolated thrombin aptamer in sterilized DI water for 3 hours (Ma and Shrotriya 2015) and then submerged in solution containing 3mM alkanethiol (6-mercapto-1-hexanol) in sterilized DI water for 1 hour, which is a sufficient time for the reaction to reach equilibrium, the derivation of this time was discuss in the introduction part (1.3).…”

“…Before experiment, the cleaned sensing cantilever was incubated in a solution containing 0.5 μM 5' thiolated thrombin aptamer in sterilized DI water for 3 hours (Ma and Shrotriya 2015) in order to immobilize thiolated aptamer on the sensing cantilever surface,. During this time period, the thiol group on aptamers will be immobilized on the gold surface through strong covalent bonds.…”

“…The thrombin aptamer cantilever (c. in figure 13) was the same as the sensing cantilever in experiment 1, that is, incubating a cleaned bare gold cantilever in a solution containing 0.5 μM 5' thiolated thrombin aptamer in sterilized DI water for 3 hours (Ma and Shrotriya 2015) and then submerged in solution containing 3mM alkanethiol (6-mercapto-1-hexanol) in sterilized DI water for 1 hour. In order to break the hybridization between neighboring aptamers on sensing cantilever, the cantilever was heated to the melting temperature of the DNA (80°C) in DI water, and slowly cooled down to room temperature.…”

“…The cantilever coated with poly A and alkanethiol (e. in figure 13) was made by incubating a cleaned bare gold cantilever in a solution containing 0.5 μM 5' thiolated 5' single stranded poly A (pHS-A30) in sterilized DI water for 3 hours (Ma and Shrotriya 2015) and then submerged in solution containing 3mM alkanethiol (6-mercapto-1-hexanol) in sterilized DI water for 1 hour.…”