Dynamic numerical simulation of a protein-ligand molecular chain connected to a moving atomic force microscope (AFM) has been studied. A sinusoidal base excitation of the cantilevered beam of the AFM is considered in some detail. A comparison between results for a single molecule and those for multiple molecules has been made. For a small number of molecules, multiple stable static equilibrium positions are observed and chaotic behavior may be generated via a period-doubling cascade for harmonic base excitation of the AFM. For many molecules in the chain, only a single static equilibrium position exists. To enable these calculations, reduced-order (dynamic) models are constructed for fully linear, combined linear/nonlinear and fully nonlinear systems. Several distinct reduced-order models have been developed that offer the option of increased computational efficiency at the price of greater effort to construct the particular reduced-order model. The agreement between the original and reduced-order models (ROM) is very good even when only one mode is included in the ROM for either the fully linear or combined linear/nonlinear systems provided the excitation frequency is lower than the fundamental natural frequency of the linear system. The computational advantage of the reduced-order model is clear from the results presented.
Dynamic Analysis of a Protein-Ligand Molecular Chain Attached to an Atomic Force Microscope
Contributed by the Technical Committee on Vibration and Sound for publication in the JOURNAL OF VIBRATION AND ACOUSTICS. Manuscript received April 2003; final revision January 2004. Associate Editor: Alexander F. Vakakis.
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Tang, D., and Dowell, E. H. (December 21, 2004). "Dynamic Analysis of a Protein-Ligand Molecular Chain Attached to an Atomic Force Microscope ." ASME. J. Vib. Acoust. October 2004; 126(4): 496–513. https://doi.org/10.1115/1.1804999
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