Manipulation of biomolecules: A molecular dynamics study

• Published in: Current applied physics 2014, 14(9), , pp.1216-1227
• Main Authors: Mahdjour Firouzi, M.A., Nejat Pishkenari, H., Mahboobi, S.H., Meghdari, A.
• Format: Article
• Language: English
• Subjects: Atomic force microscopy (AFM); Biomanipulation; Carbon nanotube (CNT) tip; Steered molecular dynamics (SMD); 물리학
• ISSN: 1567-1739; 1878-1675
• DOI: 10.1016/j.cap.2014.06.014

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 conducted to study the effects of different conditions on the success of the manipulation process. These conditions include the tip diameter, the vertical gap between the tip and substrate, and the initial orientation of the protein. Also we have studied two strategies for the manipulation of the protein by a nano-scale probe that we have named pushing and pulling. Interaction force between carbon nanotube (CNT) tips and the biomolecule, the root-mean-square deviation (RMSD), and the radius of gyration of the protein are monitored for different conditions. We found that larger tip diameters, smaller gaps between tip and substrate, and a pulling strategy increase the chance of a successful manipulation. [Display omitted] •MD simulations are used to study the manipulation of biomolecules by CNT as AFM tip.•Pushing and pulling scenarios are proposed for manipulation process.•Effect of tip diameter, tip/substrate gap and direction of protein are investigated.•Results demonstrate that the pulling scenario leads to better biomanipulations.