Contact interactions molecular dynamic simulation

Ligand-Protein Interactions The energy of formation of ligand-protein contacts can be computed as a sum of non-bonded (Lennard-Jones and electrostatic) terms similar to those used in a molecular dynamics simulation. 

Wenning and Miiser [74] extended the considerations made above for athermal, flat walls to the interaction between a curved tip and a flat substrate by including Hertzian contact mechanics. Since the Hertzian contact area A increases proportionally to they concluded that for a dry, nonadhesive, commensurate tip substrate system, Fg should scale linearly with L, since is independent of A. This has now been confirmed experimentally by Miura and Kamiya for M0S2 flakes on M0S2 surfaces [74a]. For a dry, nonadhesive, disordered tip pressed on a crystalline substrate, they obtained Fg oc which was obtained by inserting A oc into Fg oc Lfs/A. The predictions were confirmed by molecular dynamics simulations, in which special care was taken to obtain the proper contact mechanics. The results of the friction force curve are shown in Fig. 6. 

The main message of these lectures is the need to amend the classical hydrodynamic theory by direct inclusion of intermolecular interactions. This is necessary not only in the theory of contact line motion outlined here, but in all mesoscopic hydrodynamic problems, e.g. in fluid mechanics of microdevices, which attracts lately a lot of attention. The specific feature of the contact line problem is the connection between microscopic and macroscopic. The motion in the precursor film can and should be treated more precisely, on the statistical level with due account for fluctuations or directly through molecular dynamics simulations. A challenging problem is matching the microscopic theory with classical hydrodynamics applicable in macroscopic domains away from the immediate vicinity of the contact line. 

The nature of molecular dynamics simulations allows for the quantification of the number of defects formed and the determination of their exact location. These simulations show that gauche defects are formed as a result of the indentation process, as predicted by Salmeron and coworkers (4). Due to the geometry of the nanotube, these defects are localized to the region below and surrounding the tube. In addition, due to the small contact area of the nanotube used in these simulations, the number of defects formed is a function of penetration depth into the monolayer (39). Because the flexible nanotube compresses slightly as it interacts with the C13 monolayer, it does not penetrate the monolayer as deeply as a rigid nanotube. As a result, the flexible tube generates fewer defects as it indents the monolayer. 

Substantial progress in the understanding of contact interactions on the molecular level can be achieved with the use of molecular dynamic simulation. It would be worthwhile to emphasize here again some specifics of this method. 

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