Papers Published

1. Deman Tang and Dowell, E.H., Dynamic analysis of a protein-ligand molecular chain attached to an atomic force microscope, Trans. ASME. J. Vib. Acoust. (USA), vol. 126 no. 4 (2004), pp. 496 - 513 [1.1804999] .
   (last updated on 2007/04/10)

   Abstract:
   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

   Keywords:
   atomic force microscopy;linear systems;macromolecules;molecular biophysics;molecular dynamics method;nonlinear dynamical systems;proteins;reduced order systems;