Atomic force microscope experiment simulating

Molecular Dynamics Simulations of Single Molecule Atomic Force Microscope Experiments ( W. Nowak P. E. Marszalek)... 

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. 

That simulation study [49] aimed at a microscopic interpretation of single molecule atomic force microscope (AFM) experiments [50], in which unbinding forces between individual protein-ligand complexes have been m( asured... 

Visual detection of surface layers on cathodes using microscopy techniques such as SFM seems to be supportive of the existence of LiF as a particulate-type deposition.The current sensing atomic force microscope (CSAFM) technique was used by McLarnon and co-workers to observe the thin-film spinel cathode surface, and a thin, electronically insulating surface layer was detected when the electrode was exposed to either DMC or the mixture FC/DMC. The experiments were carried out at an elevated temperature (70 °C) to simulate the poor storage performance of manganese spinel-based cathodes, and degradation of the cathode in the form of disproportionation and Mn + dissolution was ob-served. °° This confirms the previous report by Taras-con and co-workers that the Mn + dissolution is acid-induced and the electrolyte solute (LiPFe) is mainly responsible. 

The atomistic structure and dynamics of the interaction of an atomic force microscopic probe (AFM) with a crystalline polyethylene surface was examined by using the molecular dynamics method coupled with ab initio quantum calculations [21]. A set of force parameters and guidelines have been derived from the extensive computer simulations, and these results were used to help explain some of the AFM images. In general, AFM experiments can be performed in a nondestructive mode with a reasonable resolution, provided that the forces of interaction between a typical-size tip and sample are kept within the... 

Because of the very large surface-area-to-volume ratios of micro-devices, adhe-sion/stiction has been considered the most important failure mode and the major obstacle for the commercialization of micro-electromechanical systems (MEMS). In this chapter, most important surface forces are introduced. The physical origin and mathematical models of these surface forces are presented. Then, adhesion effects such as wetting and surface energy, which are related to these surface forces, are extensively discussed. Self-assembled monolayers (SAMs) have recently received considerable attention as molecular-level lubricants in MEMS. The structure and the surface characteristics of SAMs are introduced. Experiments, molecular dynamics (MD) simulations, and theoretical models on the adhesion force between the atomic force microscope (AFM) tip and sample are discussed in detail. Finally, the adhesion problems related to super-hydrophobic films are discussed. 

Exploring the Scanning Probe A Simple Hands-on Experiment Simulating the Operation and Characteristics of the Atomic Force Microscope... 

The macroscopic structure of matter can be assessed, for example, by optical microscopy and can then be linked to its microscopic origin through X-ray, neutron, or electron diffraction experiments and the various forms of electron and atomic-force microscopy. A factor of 10 -10 separates the atomic, nanometer scale from the macroscopic, micrometer scale. Macroscopic dynamic techniques ultimately linked to molecular motion are, for example, dynamic mechanical and dielectric analyses and calorimetry. In order to have direct access to the details of the underlying microscopic motion, one must, however, use computational methods. A realistic microscopic description of motion has recently become possible through accurate molecular dynamics simulations and will be described in this review. It will be shown that the basic large-ampHtude molecular motion exists on a picosecond time scale (1 ps = 10 s), a ffictor at... 

In the first problem class mentioned above (hereinafter called class A), a collection of particles (atoms and/or molecules) is taken to represent a small region of a macroscopic system. In the MD approach, the computer simulation of a laboratory experiment is performed in which the "exact" dynamics of the system is followed as the particles interact according to the laws of classical mechanics. Used extensively to study the bulk physical properties of classical fluids, such MD simulations can yield information about transport processes and the approach to equilibrium (See Ref. 9 for a review) in addition to the equation of state and other properties of the system at thermodynamic equilibrium (2., for example). Current activities in this class of microscopic simulations is well documented in the program of this Symposium. Indeed, the state-of-the-art in theoretical model-building, algorithm development, and computer hardware is reflected in applications to relatively complex systems of atomic, molecular, and even macromolecular constituents. From the practical point of view, simulations of this type are limited to small numbers of particles (hundreds or thousands) with not-too-complicated inter-particle force laws (spherical syrmetry and pairwise additivity are typically invoked) for short times (of order lO" to 10 second in liquids and dense gases). 

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