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In this paper, the simulation of biomolecules manipulation using molecular dynamics (MD) is studied. In order to investigate the manipulation behavior, we have used the ubiquitin as biomolecule, a single-walled carbon nanotube (SWCNT) as manipulation probe, a two-layer graphene sheet as substrate. Along this line, a series of simulations are conducted to study the effects of different conditions on the success of manipulation process. These conditions include tip diameter, vertical gap between the tip and substrate, initial orientation of protein, and the tip position with respect to the biomolecule  

With the rapid progression of bionanorobotics, manipulation of nano-scale biosamples is becoming increasingly attractive for different biological purposes. Nevertheless, the interaction between a robotic probe and a biological sample is poorly understood and the conditions for appropriate handling is not well-known. Here, we use the molecular dynamics (MD) simulation method to investigate the manipulation process when a nanoprobe tries to move a biosample on a substrate. For this purpose, we have used Ubiquitin (UBQ) as the biomolecule, a single-walled carbon nanotube (SWCNT) as the manipulation probe, and a double-layered graphene sheets as the substrate. A series of simulations were... 

Nano-manipulation is one of the most important aspects of nano-robotics and nano-assembly. The positioning process is considered by many researches to be one of the most important parts of nano-assembly, but has been poorly investigated, particularly for biologic samples. This Letter is devoted to modelling the process of positioning a biomolecule with atomic force microscopy (AFM) in an aqueous media using molecular dynamics simulations. Carbon nanotube (CNT) and graphite sheet are selected as AFM tip and substrate, respectively. To consider the effects of the medium on the manipulation, several models for decreasing the calculations including implicit, coarse grained, and all-atom methods... 

Recently, electrode-based Dielectrophoresis (eDEP) has been used for particle manipulation by means of triangular electrodes. In this theoretical and numerical study, a microchannel with quarter-of-ellipse electrodes is presented and a detailed comparison with triangular electrodes is provided. Electric field, resultant DEP force, and particle trajectories for each microchannel are evaluated by means of COMSOL Multiphysics 4.4. Afterwards, focusing and separation efficiencies of the systems are assessed and compared. Finally, separation efficiency of our proposed model for live and dead cells is compared with that of our previous model published in the literature [1]. It is demonstrated that...