Paper Citing NAMD - Abstract
Solares, Santiago D.; Crone, Joshua C.
Real-time simulation of isolated biomolecule characterization with frequency and force modulation atomic force microscopy
JOURNAL OF PHYSICAL CHEMISTRY C, 111:10029-10034, JUL 12 2007
Recently a new AFM technique, frequency and force modulation AFM (FFM-AFM), was proposed for the characterization of delicate samples and applied within numerical simulations to calculate the cross-sectional scan of a single bacteriorhodopsin molecule with a carbon nanotube probe in air. A real-time imaging simulation of the same molecule and probe is presented here, illustrating the effect of horizontal scan speed, cantilever stiffness, effective frequency setpoint, and quality factor on the images obtained. Controls parameters are proposed for scan speeds of similar to 150 and similar to 25 nm/s in air and water, respectively. The results indicate that the most common causes leading to distorted images are excessive sample compression and denting by the tip when it approaches the sample horizontally, and loss of contact with the surface as the tip continues traveling horizontally past the sample, both of which can occur for high scan speeds and large cantilever force constants. The calculations also show that imaging conditions can be found for which the tip-sample repulsive forces and sample deformation are small and depend only weakly on imaging parameters other than scan speed.
