© The Institution of Engineering and Technology
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 have been investigated. They examined several parameters which may affect the quality of the manipulation process such as the CNT initial position with respect to the sample and substrate, its diameter and positioning strategies (pushing or pulling). The results demonstrate that despite of the implicit solvent methods, coarse-grained model can simulate the aqueous media accurately with lower computational cost. Furthermore, pulling method with a CNT which has a larger diameter and a smaller gap with respect to the substrate is the most appropriate setting for manipulation.
References
-
-
1)
-
25. Pishkenari, H.N., Meghdari, A.: ‘Investigation of the atomic-scale hysteresis in NC-AFM using atomistic dynamics’, Physica E, Low-Dimens. Syst. Nanostruct., 2010, 42, pp. 2069–2077 (doi: 10.1016/j.physe.2010.03.030).
-
2)
-
2. Lea, A., Pungor, A., Hlady, V., et al: ‘Manipulation of proteins on mica by atomic force microscopy’, Langmuir, 1992, 8, pp. 68–73 (doi: 10.1021/la00037a015).
-
3)
-
22. Pishkenari, H.N., Meghdari, A.: ‘Effects of higher oscillation modes on TM-AFM measurements’, Ultramicroscopy, 2011, 111, pp. 107–116 (doi: 10.1016/j.ultramic.2010.10.015).
-
4)
-
32. Kheirodin, M., Pishkenari, H.N., Moosavi, A., et al: ‘Study of biomolecules imaging using molecular dynamics simulations’, Nano 10, 2015, p. 1550096 (doi: 10.1142/S1793292015500964).
-
5)
-
21. Pishkenari, H.N., Meghdari, A.: ‘Surface defects characterization with frequency and force modulation atomic force microscopy using molecular dynamics simulations’, Curr. Appl. Phys., 2010, 10, pp. 583–591 (doi: 10.1016/j.cap.2009.08.002).
-
6)
-
31. Firouzi, M.M., Pishkenari, H.N., Mahboobi, S.H., et al: ‘Manipulation of biomolecules: a molecular dynamics study’, Curr. Appl. Phys., 2014, 14, (9), pp. 1216–1227 (doi: 10.1016/j.cap.2014.06.014).
-
7)
-
26. Pishkenari, H.N., Meghdari, A.: ‘Tip and sample flexibility effects on tapping mode (amplitude modulation) AFM measurements’, Micro Nano Lett. 6, 2011, 6.12, pp. 1023–1028 (doi: 10.1049/mnl.2011.0540).
-
8)
-
9. Sitti, M.: ‘Atomic force microscope probe based controlled pushing for nano-tribological characterization’, IEEE/ASME Trans. Mechatronics, 2003, 8, pp. 343–349.
-
9)
-
12. Mahboobi, S.H., Meghdari, A., Jalili, N., et al: ‘Two-dimensional atomistic simulation of metallic nanoparticles pushing’, Mod. Phys. Lett. B, 2009, 23, pp. 2695–2702 (doi: 10.1142/S0217984909020801).
-
10)
-
23. Pishkenari, H.N., Meghdari, A.: ‘Influence of the tip mass on the tip–sample interactions in TM-AFM’, Ultramicroscopy, 2011, 111, pp. 1423–1436 (doi: 10.1016/j.ultramic.2011.05.010).
-
11)
-
7. He, Y., Lu, M., Cao, J., et al: ‘Manipulating protein conformations by single-molecule AFM-FRET nanoscopy’, ACS Nano, 2012, 6, pp. 1221–1229 (doi: 10.1021/nn2038669).
-
12)
-
19. Zhang, J., Sun, T., Yan, Y.D., et al: ‘Molecular dynamics simulation of subsurface deformed layers in AFM-based nanometric cutting process’, Appl. Surf. Sci., 2008, 254, pp. 4774–4779 (doi: 10.1016/j.apsusc.2008.01.096).
-
13)
-
38. Phillips, J.C., Braun, R., Wang, W., et al: ‘Scalable molecular dynamics with NAMD’, J. Comput. Chem., 2005, 26, pp. 1781–1802 (doi: 10.1002/jcc.20289).
-
14)
-
15)
-
5. Yu, J., Moffitt, J., Hetherington, C.L., et al: ‘Mechanochemistry of a viral DNA packaging motor’, J. Mol. Biol., 2010, 400, pp. 186–203 (doi: 10.1016/j.jmb.2010.05.002).
-
16)
-
11. Mahboobi, S.H., Meghdari, A., Jalili, N., et al: ‘Qualitative study of nanocluster positioning process: planar molecular dynamics simulations’, Curr. Appl. Phys., 2009, 9, pp. 997–1004 (doi: 10.1016/j.cap.2008.10.006).
-
17)
-
29. Hamdi, M., Ferreira, A., Sharma, G., et al: ‘Prototyping bio-nanorobots using molecular dynamics simulation and virtual reality’, Microelectron. J., 2008, 39, pp. 190–201 (doi: 10.1016/j.mejo.2006.12.003).
-
18)
-
16. Mahboobi, S.H., Meghdari, A., Jalili, N., et al: ‘Molecular dynamics simulation of manipulation of metallic nanoclusters on stepped surfaces’, Central Eur. J. Phys., 2011, 9, pp. 454–465.
-
19)
-
28. Neelov, I.M., Adolf, D.B., McLeish, T.C.B., et al: ‘Molecular dynamics simulation of dextran extension by constant force in single molecule AFM’, Biophys. J., 2006, 91, pp. 3579–3588 (doi: 10.1529/biophysj.105.079236).
-
20)
-
20. Zhang, J., Sun, T., Yan, Y., et al: ‘Molecular dynamics study of scratching velocity dependency in AFM-based nanometric scratching process’, Mater. Sci. Eng. A, 2009, 505, pp. 65–69 (doi: 10.1016/j.msea.2008.10.049).
-
21)
-
18. Zhu, P.-Z., Hu, Y., Ma, T., et al: ‘Study of AFM-based nanometric cutting process using molecular dynamics’, Appl. Surf. Sci., 2010, 256, pp. 7160–7165 (doi: 10.1016/j.apsusc.2010.05.044).
-
22)
-
1. Pakes, C.I., George, D.P., Ramelow, S., et al: ‘Manipulation of single magnetic protein particles using atomic force microscopy’, J. Magn. Magn. Mater., 2004, 272, pp. E1231–E1233 (doi: 10.1016/j.jmmm.2003.12.299).
-
23)
-
10. Butt, H.-J., Cappella, B., Kappl, M.: ‘Force measurements with the atomic force microscope: technique, interpretation and applications’, Surf. Sci. Rep., 2005, 59, pp. 1–152 (doi: 10.1016/j.surfrep.2005.08.003).
-
24)
-
25)
-
30. Masugata, K., Ikai, A., Okazaki, S., et al: ‘Molecular dynamics study of mechanical extension of polyalanine by AFM cantilever’, Appl. Surf. Sci., 2002, 188, pp. 372–376 (doi: 10.1016/S0169-4332(01)00954-0).
-
26)
-
24. Pishkenari, H.N., Mahboobi, S.H., Meghdari, A., et al: ‘Simulation of imaging in tapping-mode atomic-force microscopy: a comparison amongst a variety of approaches’, J. Phys. D, Appl. Phys., 2011, 44.7, p. 075303 (doi: 10.1088/0022-3727/44/7/075303).
-
27)
-
33. Arkhipov, A., Roos, W.H., Wuite, G.J.L., et al: ‘Elucidating the mechanism behind irreversible deformation of viral capsids’, Biophys. J., 2009, 97, pp. 2061–2069 (doi: 10.1016/j.bpj.2009.07.039).
-
28)
-
36. Chen, L., Cheung, C.L., Ashby, P.D., et al: ‘Single-walled carbon nanotube AFM probes: optimal imaging resolution of nanoclusters and biomolecules in ambient and fluid environments’, Nano Lett., 2004, 4, pp. 1725–1731 (doi: 10.1021/nl048986o).
-
29)
-
8. Sitti, M.: ‘Survey of nanomanipulation systems’. Proc. of the 2001 First IEEE Conf. on Nanotechnology, 2001. IEEE-NANO 2001, 2001, pp. 75–80.
-
30)
-
40. Marrink, S.J., Risselada, H.J., Yefimov, S., et al: ‘The MARTINI force field: coarse grained model for biomolecular simulations’, J. Phys. Chem. B, 2007, 111, pp. 7812–7824 (doi: 10.1021/jp071097f).
-
31)
-
27. Pishkenari, H.N.: ‘Atomic interactions between metallic tips and surfaces in NC-AFM’, J. Phys. D, Appl. Phys., 2015, 48.12, p. 125301 (doi: 10.1088/0022-3727/48/12/125301).
-
32)
-
4. Zohar, H., Hetherington, C.L., Bustamante, C., et al: ‘Peptide nucleic acids as tools for single-molecule sequence detection and manipulation’, Nano Lett., 2010, 10, pp. 4697–4701 (doi: 10.1021/nl102986v).
-
33)
-
37. Frank, I., Tanenbaum, D.: ‘Mechanical properties of suspended graphene sheets’, J. Vac. Sci. Technol. B, 2007, 25, pp. 2558–2561 (doi: 10.1116/1.2789446).
-
34)
-
15. Mahboobi, S.H., Meghdari, A., Jalili, N., et al: ‘Planar molecular dynamics simulation of Au clusters in pushing process’, Int. J. Nanomanuf., 2010, 5, pp. 288–296 (doi: 10.1504/IJNM.2010.033871).
-
35)
-
17. Zhu, P.-Z., Hu, Y., Wang, H., et al: ‘Study of effect of indenter shape in nanometric scratching process using molecular dynamics’, Mater. Sci. Eng. A, 2011, 528, pp. 4522–4527 (doi: 10.1016/j.msea.2011.02.035).
-
36)
-
14. Mahboobi, S.H., Meghdari, A., Jalili, N., et al: ‘Molecular dynamics simulation of manipulation of metallic nanoclusters on double-layer substrates’, Physica E, Low-Dimens. Syst. Nanostruct., 2010, 42, pp. 2364–2374 (doi: 10.1016/j.physe.2010.05.018).
-
37)
-
13. Mahboobi, S.H., Meghdari, A., Jalili, N., et al: ‘Precise positioning and assembly of metallic nanoclusters as building blocks of nanostructures: a molecular dynamics study’, Physica E, Low-Dimens. Syst. Nanostruct., 2009, 42, pp. 182–195 (doi: 10.1016/j.physe.2009.10.008).
-
38)
-
3. Fotiadis, D., Scheuring, S., Müller, S.A., et al: ‘Imaging and manipulation of biological structures with the AFM’, Micron, 2002, 33, pp. 385–397 (doi: 10.1016/S0968-4328(01)00026-9).
-
39)
-
34. Woolley, A.T., Cheung, C.L., Hafner, J.H., et al: ‘Structural biology with carbon nanotube AFM probes’, Chem. Biol., 2000, 7, pp. R193–R204 (doi: 10.1016/S1074-5521(00)00037-5).
-
40)
-
6. Hards, A., Zhou, C., Seitz, M., et al: ‘Simultaneous AFM manipulation and fluorescence imaging of single DNA strands’, ChemPhysChem, 2005, 6, pp. 534–540 (doi: 10.1002/cphc.200400515).
http://iet.metastore.ingenta.com/content/journals/10.1049/mnl.2015.0070
Related content
content/journals/10.1049/mnl.2015.0070
pub_keyword,iet_inspecKeyword,pub_concept
6
6