Single-molecule methods atomic force microscope

As well as visualisation, quantitative measurements are necessary in order to understand the adhesion process. One possible method involves streaming the cells over a surface and measuring the maximum speed of flow at which adhesion can occur [see 64]. Another technique uses the atomic force microscope for measurements at a single molecule [66]. 

The atomic force microscope (AFM) is not only a formidable instrument to image surfaces and immobilized supramolecular structures at very high spatial resolution but it is also a very interesting tool to quantitatively measure interaction forces. It is fair to conclude that AFM-based single-molecule force spectroscopy (SMFS) has matured in the past decade to become a reliable method to probe the rupture of individual supramolecular bonds and to analyze the strength of noncovalent interactions in a wide range... 

Figures 13.15 and 13.16 show two examples that underline the flexibility and robustness of this technique for nanofabrication. Figure 13.15a shows the steps to build molecular architectures by combining top-down nanolithography and self-assembled methods. In this case, single molecules of ferritin have been deposited on silicon surfaces with an accuracy similar to the size of the molecules (r IO nm. First, the silicon surface is covered with a self-assembled monolayer of aminopropyltriethoxysilane (APTES), and then a region is locally oxidized with the atomic force microscope tip. The oxidation process also removes the monolayer under the tip. The nanostripe before the deposition of ferritin molecules is shown in Fig. 13.15b, while Fig. 13.15c shows a densely packed distribution of proteins on the nanostripe. The...

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. 

DPD was originally developed by Hoogerbrugge and Koelman [27]. It can simulate both Newtonian and non-Newtonian fluids, including polymer melts and blends, on microscopic length and time scales. Like MD and BD, DPD is a particle-based method. However, its basic unit is not a single atom or molecule but a molecular assembly (i.e., a partiele).DPD particles are defined by then-mass M, position r. and momentum P. The interaction force between two DPD particles i and j can be described by a sum of conservative, dissipative and random forces F, [28-30]... 

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