Atomic force microscopy dynamic processes

Abstract. Molecular dynamics (MD) simulations of proteins provide descriptions of atomic motions, which allow to relate observable properties of proteins to microscopic processes. Unfortunately, such MD simulations require an enormous amount of computer time and, therefore, are limited to time scales of nanoseconds. We describe first a fast multiple time step structure adapted multipole method (FA-MUSAMM) to speed up the evaluation of the computationally most demanding Coulomb interactions in solvated protein models, secondly an application of this method aiming at a microscopic understanding of single molecule atomic force microscopy experiments, and, thirdly, a new method to predict slow conformational motions at microsecond time scales. 

PMMA) was employed. In addition, atomic force microscopy is used for a more quantitative read-out of the PMMA. Since it is a two-step process - an image formation step on the photoresist followed by a magnification of the miniature contact print formed on the resist - it is difficult to use in the study of dynamic processes. The use of flash sources such as X-ray lasers or laser-produced plasmas in addition to the use of synchrotron radiation sources increased the activity of X-ray contact imaging, allowing the capture of the image on a nanosecond time scale. 

Shibata M, Yamashita H, Uchihashi T, Kandori H, Ando T (2010) High speed atomic force microscopy shows dynamic molecular processes in photoactivated bacteriorhodopsin. Nat Nanotechnol 5 208-212... 

This article presents recent progress in high-speed atomic force microscopy for dynamic imaging of biomolecular processes, including the theoretical basis for the highest possible imaging rate, instrumentation, hydrodynamic effects on cantilever oscillation, and various visualization studies on the dynamic molecular process and structure of proteins. 

T. Ando, T. Uchihashi, and T. Fukuma, High-speed atomic force microscopy for nano-visualization of dynamic biomolecular processes. Prog. Surf. Sci., 83, 337 (2008). 

M. Shibata, H. Yamashita, T. Uchlhashi, H. Kandori, and T. Ando, Highspeed atomic force microscopy shows dynamic molecular processes in photo-activated bacteriorhodopsin, Nat Nanotech., 5, 208 (2010]. 

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