Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Optomechanical detection of vibration modes of a single bacterium

A Publisher Correction to this article was published on 29 April 2020

This article has been updated


Low-frequency vibration modes of biological particles, such as proteins, viruses and bacteria, involve coherent collective vibrations at frequencies in the terahertz and gigahertz domains. These vibration modes carry information on their structure and mechanical properties, which are good indicators of their biological state. In this work, we harnessed a particular regime in the physics of coupled mechanical resonators to directly measure these low-frequency mechanical resonances of a single bacterium. We deposit the bacterium on the surface of an ultrahigh frequency optomechanical disk resonator in ambient conditions. The vibration modes of the disk and bacterium hybridize when their associated frequencies are similar. We developed a general theoretical framework to describe this coupling, which allows us to retrieve the eigenfrequencies and mechanical loss of the bacterium low-frequency vibration modes (quality factor). Additionally, we analysed the effect of hydration on these vibrational modes. This work demonstrates that ultrahigh frequency optomechanical resonators can be used for vibrational spectrometry with the unique capability to obtain information on single biological entities.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Prices vary by article type



Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Fundamental vibration modes of biological particles and optomechanical disk resonators at the gigahertz regime.
Fig. 2: Stochastic response of a sensing damped harmonic oscillator coupled in series to an analyte that exhibits two orthogonal vibration modes, represented as two damped harmonic oscillators.
Fig. 3: Numerical calculation of the mechanical coupling of the bacterium and the disk resonator.
Fig. 4: Effect of hydration on the vibration mode of a bacterium.

Data availability

The data that support the plots within this paper and other findings of this study are available from the corresponding author upon reasonable request

Change history


  1. Smith, E. & Dent, G. Modern Raman Spectroscopy: A Practical Approach (Wiley, 2019).

  2. Davydov, A. S. The theory of contraction of proteins under their excitation. J. Theor. Biol. 38, 559–569 (1973).

    Article  CAS  Google Scholar 

  3. Hay, S. & Scrutton, N. S. Good vibrations in enzyme-catalysed reactions. Nat. Chem. 4, 161–168 (2012).

    Article  CAS  Google Scholar 

  4. Ford, L. H. Estimate of the vibrational frequencies of spherical virus particles. Phys. Rev. E 67, 051924 (2003).

    Article  CAS  Google Scholar 

  5. Sirotkin, S., Mermet, A., Bergoin, M., Ward, V. & Van Etten, J. L. Viruses as nanoparticles: structure versus collective dynamics. Phys. Rev. E 90, 022718 (2014).

    Article  CAS  Google Scholar 

  6. Zinin, P., Allen, J. S. III & Levin, V. Mechanical resonances of bacteria cells. Phys. Rev. E 72, 061907 (2005).

    Article  CAS  Google Scholar 

  7. Turton, D. A. et al. Terahertz underdamped vibrational motion governs protein–ligand binding in solution. Nat. Commun. 5, 3999 (2014).

    Article  CAS  Google Scholar 

  8. Acbas, G., Niessen, K. A., Snell, E. H. & Markelz, A. G. Optical measurements of long-range protein vibrations. Nat. Commun. 5, 3076 (2014).

    Article  Google Scholar 

  9. Longo, G. et al. Antibiotic-induced modifications of the stiffness of bacterial membranes. J. Microbiol. Methods 93, 80–84 (2013).

    Article  CAS  Google Scholar 

  10. Köhler, J. et al. Mutation of the myosin converter domain alters cross-bridge elasticity. Proc. Natl Acad. Sci. USA 99, 3557–3562 (2002).

    Article  Google Scholar 

  11. Greber, U. F. Virus and host mechanics support membrane penetration and cell entry. J. Virol. 90, 3802–3805 (2016).

    Article  CAS  Google Scholar 

  12. Roos, W. H., Bruinsma, R. & Wuite, G. J. L. Physical virology. Nat. Phys. 6, 733–743 (2010).

    Article  CAS  Google Scholar 

  13. Malvar, O. et al. Mass and stiffness spectrometry of nanoparticles and whole intact bacteria by multimode nanomechanical resonators. Nat. Commun. 7, 13452 (2016).

    Article  CAS  Google Scholar 

  14. Dexheimer, S. L. Terahertz Spectroscopy: Principles and Applications (CRC, 2007).

  15. Stephanidis, B., Adichtchev, S., Gouet, P., McPherson, A. & Mermet, A. Elastic properties of viruses. Biophys. J. 93, 1354–1359 (2007).

    Article  CAS  Google Scholar 

  16. Zinin, P. V. & Allen, J. S. III Deformation of biological cells in the acoustic field of an oscillating bubble. Phys. Rev. E 79, 021910 (2009).

    Article  Google Scholar 

  17. Favero, I. & Karrai, K. Optomechanics of deformable optical cavities. Nat. Photon. 3, 201–205 (2009).

    Article  CAS  Google Scholar 

  18. Ding, L. et al. High frequency GaAs nano-optomechanical disk resonator. Phys. Rev. Lett. 105, 263903 (2010).

    Article  Google Scholar 

  19. Gil-Santos, E. et al. High-frequency nano-optomechanical disk resonators in liquids. Nat. Nanotechnol. 10, 810–816 (2015).

    Article  CAS  Google Scholar 

  20. Baker, C. et al. Photoelastic coupling in gallium arsenide optomechanical disk resonators. Opt. Express 22, 14072–14086 (2014).

    Article  Google Scholar 

  21. Hanay, M. S. et al. Single-protein nanomechanical mass spectrometry in real time. Nat. Nanotechnol. 7, 602–608 (2012).

    Article  CAS  Google Scholar 

  22. Dominguez-Medina, S. et al. Neutral mass spectrometry of virus capsids above 100 megadaltons with nanomechanical resonators. Science 362, 918–922 (2018).

    Article  CAS  Google Scholar 

  23. Liu, F., Alaie, S., Leseman, Z. C. & Hossein-Zadeh, M. Sub-pg mass sensing and measurement with an optomechanical oscillator. Opt. Express 21, 19555–19567 (2013).

    Article  Google Scholar 

  24. Kosaka, P. M., Calleja, M. & Tamayo, J. Optomechanical devices for deep plasma cancer proteomics. Semin. Cancer Biol. 52, 26–38 (2018).

    Article  CAS  Google Scholar 

  25. Spletzer, M., Raman, A., Wu, A. Q., Xu, X. & Reifenberger, R. Ultrasensitive mass sensing using mode localization in coupled microcantilevers. Appl. Phys. Lett. 88, 254102 (2006).

    Article  Google Scholar 

  26. Gil-Santos, E. et al. Mass sensing based on deterministic and stochastic responses of elastically coupled nanocantilevers. Nano Lett. 9, 4122–4127 (2009).

    Article  CAS  Google Scholar 

  27. Gil-Santos, E., Ramos, D., Pini, V., Calleja, M. & Tamayo, J. Exponential tuning of the coupling constant of coupled microcantilevers by modifying their separation. Appl. Phys. Lett. 98, 123108 (2011).

    Article  Google Scholar 

  28. Stassi, S. et al. Large-scale parallelization of nanomechanical mass spectrometry with weakly-coupled resonators. Nat. Commun. 10, 3647 (2019).

    Article  Google Scholar 

  29. Duval, E. Far-infrared and Raman vibrational transitions of a solid sphere: selection rules. Phys. Rev. B 46, 5795–5797 (1992).

    Article  CAS  Google Scholar 

  30. Ruz, J. J., Tamayo, J., Pini, V., Kosaka, P. M. & Calleja, M. Physics of nanomechanical spectrometry of viruses. Sci. Rep. 4, 6051 (2014).

    Article  CAS  Google Scholar 

  31. Furusawa, H., Sekine, T. & Ozeki, T. Hydration and viscoelastic properties of high-and low-density polymer brushes using a quartz-crystal microbalance based on admittance analysis (QCM-A). Macromolecules 49, 3463–3470 (2016).

    Article  CAS  Google Scholar 

  32. Domínguez, C. M. et al. Effect of water–DNA interactions on elastic properties of DNA self-assembled monolayers. Sci. Rep. 7, 536 (2017).

    Article  Google Scholar 

  33. Bateman, J. B., Stevens, C. L., Mercer, W. B. & Carstensen, E. L. Relative humidity and the killing of bacteria: the variation of cellular water content with external relative humidity or osmolality. Microbiology 29, 207–219 (1962).

    CAS  Google Scholar 

  34. Rubel, G. O. Measurement of water vapor sorption by single biological aerosols. Aerosol Sci. Tech. 27, 481–490 (1997).

    Article  CAS  Google Scholar 

  35. Deng, Y., Sun, M. & Shaevitz, J. W. Direct measurement of cell wall stress stiffening and turgor pressure in live bacterial cells. Phys. Rev. Lett. 107, 158101 (2011).

    Article  Google Scholar 

  36. Nikiyan, H., Vasilchenko, A. & Deryabin, D. Humidity-dependent bacterial cells functional morphometry investigations using atomic force microscope. Int. J. Microbiol. 2010, 704170 (2010).

    Article  Google Scholar 

  37. Thwaites, J. J. & Surana, U. C. Mechanical properties of Bacillus subtilis cell walls: effects of removing residual culture medium. J. Bacteriol. 173, 197–203 (1991).

    Article  CAS  Google Scholar 

  38. Kulasinski, K., Guyer, R., Keten, S., Derome, D. & Carmeliet, J. Impact of moisture adsorption on structure and physical properties of amorphous biopolymers. Macromolecules 48, 2793–2800 (2015).

    Article  CAS  Google Scholar 

  39. Guillet, Y., Abbas, A., Ravaine, S. & Audoin, B. Ultrafast microscopy of the vibrational landscape of a single nanoparticle. Appl. Phys. Lett. 114, 091904 (2019).

    Article  Google Scholar 

  40. Hsueh, C.-C., Gordon, R. & Rottler, J. Dewetting during terahertz vibrations of nanoparticles. Nano Lett. 18, 773–777 (2018).

    Article  CAS  Google Scholar 

Download references


This work was supported by the European Union’s Horizon 2020 research and innovation program under grant agreement no. 731868 – VIRUSCAN and European Research Council grants 681275 – LIQUIDMASS- ERC- CoG-2015 and 770933-NOMLI-ERC-CoG 2017, by the Spanish Science, Innovation and Universities Ministry through project CELLTANGLE reference RTI2018-099369-B-I00 and Ramón y Cajal grant RYC-2017-21640 to P.M.K. and by the Comunidad de Madrid (iLUNG B2017/BMD-3884) with support from the EU (FEDER, FSE). We acknowledge J. Mingorance for guidance and for providing the bacterial samples. All the authors acknowledge service from the IMN X-SEM Laboratory, which is funded by MCIU (project CSIC13-4E-1794) and the EU (FEDER, FSE). E.G.S. acknowledges financial support by the Fundación General CSIC (Programa ComFuturo), as well as Marie-Sklodowska Curie Actions (H2020-MSCA-IF-2015) under the NOMBIS project (703354).

Author information

Authors and Affiliations



E.G.-S., M.C. and J.T. conceived and designed the experiments, E.G.-S. and O.M. performed the experiments, E.G.-S., J.J.R. and J.T. analysed the data and developed the theory, S.G.-L., O.M. and P.M.K. contributed materials and tools to deposit the bacteria, E.G.-S., A.L. and I.F. designed and fabricated the devices and J.T., M.C. and E.G.-S. co-wrote the paper. All the authors discussed the results and commented on the manuscript.

Corresponding authors

Correspondence to Eduardo Gil-Santos or Javier Tamayo.

Ethics declarations

Competing interests

E.G.-S., J.J.R., O.M., M.C. and J.T. are inventors of a related patent (WO/2019/229000) owned by their host institution Consejo Superior de Investigaciones Científicas.

Additional information

Peer review information Nature Nanotechnology thanks Carlo Ricciardi, Yun-Feng Xiao and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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

Supplementary information

Supplementary Information

Supplementary Materials and Methods, Figs. 1–4 and refs. 1–7.

Rights and permissions

Reprints and Permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Gil-Santos, E., Ruz, J.J., Malvar, O. et al. Optomechanical detection of vibration modes of a single bacterium. Nat. Nanotechnol. 15, 469–474 (2020).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


Quick links

Find nanotechnology articles, nanomaterial data and patents all in one place. Visit Nano by Nature Research