Skip to main content
SpringerLink
Log in

AFM-based manipulation modeling of bacillus subtilis bioparticles using finite element method

  • Original
  • Published:
Archive of Applied Mechanics Aims and scope Submit manuscript

Abstract

Since bioparticles experience large deformations, it is imperative to develop an appropriate model for particle modeling based on its size to prevent Nano biological particle destruction such as Bacillus, which is modeled as a Nano-beam. In this paper, models with large deformation assumptions were suggested for a longitudinal particle that can be geometrically considered as a beam. By modeling a nano/microparticle using continuum mechanics theory and dynamic simulation based on FEM, the dynamic behavior and shape deformation caused by the manipulation forces were examined. Hence, the manipulation of bioparticles with a cylindrical shape, named Bacillus Subtilis, was investigated. Critical time and forces and the predominant mode of movement of biological nanoparticles in a manipulation process were obtained and the Euler–Bernoulli theory was utilized to investigate the dynamic of biological nanoparticles. After the discretization of governing equations of motion using the Galerkin method, mass and stiffness matrices were extracted and critical forces were calculated to examine the dynamic behavior of particles. The effect of the aspect ratio showed that the deformation of the particle increases with increasing aspect ratio. In addition, the manipulation force is an essential parameter when small and large deflection models are compared. It was evident that the difference between linear and nonlinear deflection models at L/D = 100 was decreased from 39.47% for the 10 µN force to 12.46% for the 5 µN force. It was deduced that the small and large deflection models tend to have similar results with reducing force.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9
Fig. 10
Fig. 11
Fig. 12
Fig. 13
Fig. 14

Similar content being viewed by others

References

  1. Tafazzoli, A., Sitti, M.: Dynamic modes of nanoparticle motion during nanoprobe-based manipulation. In: 4th IEEE Conference on Nanotechnology, pp. 35–37. IEEE (2004)

  2. Fotiadis, D., Scheuring, S., Müller, S.A., Engel, A., Müller, D.J.: Imaging and manipulation of biological structures with the AFM. Micron 33, 385–397 (2002). https://doi.org/10.1016/S0968-4328(01)00026-9

    Article  Google Scholar 

  3. Tsapikouni, T.S., Missirlis, Y.F.: Measuring the force of single protein molecule detachment from surfaces with AFM. Colloids Surfaces B Biointerfaces 75, 252–259 (2010). https://doi.org/10.1016/j.colsurfb.2009.08.041

    Article  Google Scholar 

  4. Shen, Y., Nakajima, M., Ridzuan Ahmad, M., Kojima, S., Homma, M., Fukuda, T.: Effect of ambient humidity on the strength of the adhesion force of single yeast cell inside environmental-SEM. Ultramicroscopy 111, 1176–1183 (2011). https://doi.org/10.1016/j.ultramic.2011.02.008

    Article  Google Scholar 

  5. Li, M., Liu, L., Xi, N., Wang, Y., Dong, Z., Xiao, X., Zhang, W.: Atomic force microscopy imaging and mechanical properties measurement of red blood cells and aggressive cancer cells. Sci. China Life Sci. 55, 968–973 (2012). https://doi.org/10.1007/s11427-012-4399-3

    Article  Google Scholar 

  6. Korayem, M.H., Khaksar, H., Taheri, M.: Modeling of contact theories for the manipulation of biological micro/nanoparticles in the form of circular crowned rollers based on the atomic force microscope. J. Appl. Phys. 114, 183715 (2013). https://doi.org/10.1063/1.4829919

    Article  Google Scholar 

  7. Korayem, M.H., Mahmoodi, Z., Taheri, M., Saraee, M.: Three-dimensional modeling and simulation of the AFM-based manipulation of spherical biological micro/nanoparticles with the consideration of contact mechanics theories. Proc. Inst. Mech. Eng. Part K J. Multi-Body Dyn. 229, 370–382 (2015). https://doi.org/10.1177/1464419314567551

    Article  Google Scholar 

  8. Kasas, S., Longo, G., Dietler, G.: Mechanical properties of biological specimens explored by atomic force microscopy. J. Phys. D. Appl. Phys. 46, 133001 (2013)

    Article  Google Scholar 

  9. Korayem, M.H., Badkoobeh Hezaveh, H., Taheri, M.: Dynamic modeling and simulation of rough cylindrical micro/nanoparticle manipulation with atomic force microscopy. Microsc. Microanal. 20, 1692–1707 (2014). https://doi.org/10.1017/S1431927614013233

    Article  Google Scholar 

  10. Ikai, A., Afrin, R., Saito, M., Watanabe-Nakayama, T.: Atomic force microscope as a nano- and micrometer scale biological manipulator: a short review. Semin. Cell Dev. Biol. (2017). https://doi.org/10.1016/j.semcdb.2017.07.031

    Article  Google Scholar 

  11. Tang, G., Galluzzi, M., Biswas, S., Stadler, F.J.: microscopy and finite element simulations Investigation of micromechanical properties of hard sphere filled composite hydrogels by atomic force microscopy and finite element simulations. J. Mech. Behav. Biomed. Mater. (2017). https://doi.org/10.1016/j.jmbbm.2017.10.035

    Article  Google Scholar 

  12. Rawal, B.D.: ‘“ Nanobacterium sanguineum ”’–Is it a new life-form in search of human ailment or commensal : Overview of its transmissibility and chemical means of intervention. pp. 1062–1066 (2005). https://doi.org/10.1016/j.mehy.2005.06.024

  13. Yao, X., Walter, J., Burke, S., Stewart, S., Jericho, M.H., Pink, D.: Atomic force microscopy and theoretical considerations of surface properties and turgor pressures of bacteria. Colloids Surfaces B Biointerfaces 23, 213–230 (2002)

    Article  Google Scholar 

  14. Yamashita, H., Taoka, A., Uchihashi, T., Asano, T., Ando, T., Fukumori, Y.: Single-molecule imaging on living bacterial cell surface by high-speed AFM. J. Mol. Biol. 422, 300–309 (2012). https://doi.org/10.1016/j.jmb.2012.05.018

    Article  Google Scholar 

  15. Korayem, M.H., Hoshiar, A.K., Ghofrani, M.: Comprehensive modelling and simulation of cylindrical nanoparticles manipulation by using a virtual reality environment. J. Mol. Graph. Model. 75, 266–276 (2017)

    Article  Google Scholar 

  16. Saraee, M.B., Korayem, M.H.: Dynamic simulation and modeling of the motion modes produced during the 3D controlled manipulation of biological micro/nanoparticles based on the AFM. J. Theor. Biol. 378, 65–78 (2015). https://doi.org/10.1016/j.jtbi.2015.04.021

    Article  MathSciNet  MATH  Google Scholar 

  17. Moshirpanahi, A., Haghighi, S.E., Imam, A.: Dynamic modeling of a cylindrical nanoparticle manipulation by AFM. Eng. Sci. Technol. Int. J. 24, 611–619 (2021)

    Google Scholar 

  18. Moradi, M., Fereidon, A.H., Sadeghzadeh, S.: Dynamic modeling for nanomanipulation of polystyrene nanorod by atomic force microscope. Sci. Iran. 18, 808–815 (2011). https://doi.org/10.1016/j.scient.2011.06.003

    Article  Google Scholar 

  19. Moradi, M., Fereidon, A.H., Sadeghzadeh, S.: Aspect ratio and dimension effects on nanorod manipulation by atomic force microscope. IET Micro Nano Lett. 5, 324–327 (2010)

    Article  Google Scholar 

  20. Korayem, M.H., Zakeri, M.: Sensitivity analysis of nanoparticles pushing critical conditions in 2-D controlled nanomanipulation based on AFM. Int. J. Adv. Manuf. Technol. 41, 714–726 (2009). https://doi.org/10.1007/s00170-008-1519-0

    Article  Google Scholar 

  21. Korayem, M.H., Saraee, M.B., Mahmoodi, Z., Dehghani, S.: Modeling and simulation of three dimensional manipulations of biological micro/nanoparticles by applying cylindrical contact mechanics models by means of AFM. J. Nanoparticle Res. 17, 439 (2015)

    Article  Google Scholar 

  22. Israelachvili, J.N.: Intermolecular and surface forces. Academic press (2011)

  23. Johnson, K.L., Kendall, K.: Roberts, aAD: surface energy and the contact of elastic solids. Proc. R. Soc. London A. Math. Phys. Sci. 324, 301–313 (1971)

    Google Scholar 

  24. Lundberg, V.G.: Elastische berührung zweier halbräume. Forsch. Gebiet Ing. A 10, 201–211 (1939)

    Article  MATH  Google Scholar 

  25. Reddy, J.N.: An introduction to nonlinear finite element analysis second edition: with applications to heat transfer, fluid mechanics, and solid mechanics. OUP Oxford (2014)

  26. Walters, D.A., Cleveland, J.P., Thomson, N.H., Hansma, P.K., Wendman, M.A., Gurley, G., Elings, V.: Short cantilevers for atomic force microscopy. Rev. Sci. Instrum. 67, 3583–3590 (1996)

    Article  Google Scholar 

  27. Chao, Y., Zhang, T.: Optimization of fixation methods for observation of bacterial cell morphology and surface ultrastructures by atomic force microscopy. Appl. Microbiol. Biotechnol. (2011). https://doi.org/10.1007/s00253-011-3551-5

    Article  Google Scholar 

  28. Moloney, M., Mcdonnell, L., Shea, H.O.: Atomic force microscopy of BHK-21 cells : an investigation of cell fixation techniques. Ultramicroscopy 100, 153–161 (2004). https://doi.org/10.1016/j.ultramic.2003.12.010

    Article  Google Scholar 

Download references

Funding

The authors did not receive support from any organization for the submitted work.

Author information

Authors and Affiliations

  1. Robotics Research Laboratory, Center of Excellence in Experimental Solid Mechanics and Dynamics, School of Mechanical Engineering, Iran University of Science and Technology, P. O. Box 16846-1311, Tehran, Iran

    Moharam Habibnejad Korayem, Zahra Reisi & Rouzbeh Nouhi Hefzabad

Authors
  1. Moharam Habibnejad Korayem
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Zahra Reisi
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Rouzbeh Nouhi Hefzabad
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Moharam Habibnejad Korayem.

Ethics declarations

Conflicts of interests

The authors declare that they have no competing financial and non-financial interests.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Korayem, M.H., Reisi, Z. & Hefzabad, R.N. AFM-based manipulation modeling of bacillus subtilis bioparticles using finite element method. Arch Appl Mech 93, 2891–2906 (2023). https://doi.org/10.1007/s00419-023-02416-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00419-023-02416-1

Keywords

Search

Navigation