Manipulation with atomic force microscopy: DNA and yeast micro/nanoparticles in biological environments

Abstract

Although significant attempts have been made to automate the manipulation of biological cells with atomic force microscopy, these efforts have faced many limitations and restrictions. Researchers have recently tried to measure the interacting forces in order to improve the reliability of manipulation operations with atomic force microscopy. By manipulation of micro/nanoparticles of different materials and shapes, as the target particles, in different biological environments, the interacting forces existing between these micro/nanoparticles and the biological environment will be different from those in the air medium. Therefore, in this paper, first, a general overview and simulation of the important forces acting in the biological environment was presented, and forces such as the adhesion force, hydration force and the electrostatic double-layer force were modeled and simulated in different environments (e.g. water, alcohol and blood plasma). After different biological environments (in comparison with the air medium) were explored and modeled, the manipulation operations with atomic force microscopy were simulated for different micro/nanoparticles such as gold, DNA and yeast by considering the forces existing in various biological environments. The results of manipulation in this paper indicate that in the air and liquid environments, the biological particles (DNA and yeast) will start to move after a longer time and by a higher magnitude force relative to the gold particles. This outcome is predictable, given the properties and stickiness of the biological particles. Also by comparing the obtained results, it is found that the critical force and critical time of manipulation with atomic force microscopy for gold nanoparticles slightly increase in water relative to air, which can be due to the properties of water and the existing forces in water that resist against the movement of nanoparticles. Finally, the obtained results were compared with the available empirical results. It can be seen that the obtained simulation values have a good correlation with the empirical results. The closeness of these two values confirms the validity of the performed simulation.

Effect of surface topography upon micro-impact dynamics

“…The current study is generic for the problems of similar physical scale, such as for micro-gears presented in [4] as well as manipulation of nano and micro-biological particles such as yeast, various proteins and even blood cells, using an atomic force microscope in dry or wet environment [32,33]. The impact of any pair of solids of revolution can be reduced to an equivalent ellipsoidal solid against a flat plane as originally expounded by the Hertzian contact mechanics.…”

A general formulation of quality factor for composite micro/nano beams in the air environment based on the nonlocal elasticity theory

“…In addition, the first three natural frequencies and the non-dimensional parameters i n,  of the nonlocal beam with two sections are presented in table (6). As it can be seen from table (6), the changing range of the natural frequencies of the nonlocal beam is too wide and this matter increases the complexity and computation of the problem dramatically.…”

“…These innovative small structures exhibit essential and imperative role in the modern technologies because their mechanical features are extremely improved by decreasing their dimensions. Therefore, these small structures are widely implemented in several micro/nano systems such as atomic force microscope (AFM), micro/nano switches, micro/nano resonators and bio-sensors [5][6][7][8]. Currently, micro/nano beam-like structures are identified as basic constituents of these small systems because of several problems in manufacturing joints in micro-tonano scale [9].…”

Investigating the effective parameters in the Atomic Force Microscope–based dynamic manipulation of rough micro/nanoparticles by using the Sobol sensitivity analysis method

“…In these works, the dynamic model of the process has been presented as the principal means of dynamically studying the manipulation process, and various models have been developed for different geometrical conditions of the target particle and different mediums in which the AFM is utilized during the manipulation. 5,8,15…”