Skip to main content Accessibility help

We use cookies to distinguish you from other users and to provide you with a better experience on our websites. Close this message to accept cookies or find out how to manage your cookie settings.

Close cookie message
×
Hostname: page-component-848d4c4894-4rdrl Total loading time: 0 Render date: 2024-06-26T15:28:10.521Z Has data issue: false hasContentIssue false

5 - Scanning Probe Microscopy

from Part III - Imaging Techniques

Published online by Cambridge University Press:  06 July 2019

By
Adam F. Wallace
Edited by
Janice P. L. Kenney ,
Harish Veeramani  and
Daniel S. Alessi
Janice P. L. Kenney
Affiliation:
MacEwan University, Edmonton
Harish Veeramani
Affiliation:
Carleton University, Ottawa
Daniel S. Alessi
Affiliation:
University of Alberta
Get access

Summary

Scanning probe microscopy (SPM) is a suite of related imaging methods, in which variations in the interaction force between a probe and a sample surface are used to generate image contrast. These instruments are incredibly sensitive; they can measure forces on the order of those required to break physical and chemical bonds, and under the most optimal conditions, atomic-scale resolution can be achieved. Although SPM is still primarily used for imaging, it is increasingly being used to measure nanoscale properties and interaction forces. This chapter serves as an introduction to the fundamentals of SPM and to the most prevalent methods needed for the investigation of mineral–microbe interactions.

Type
Chapter
Information
Analytical Geomicrobiology
A Handbook of Instrumental Techniques
 , pp. 121 - 147
Publisher: Cambridge University Press
Print publication year: 2019

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

5.8 References

Abelmann, L., van den Bos, A. and Lodder, C. (2005) ‘Magnetic Force Microscopy – Towards Higher Resolution’, in Hopster, H. and Oepen, H. P. (eds) Magnetic Microscopy of Nanostructures. Berlin, Heidelberg: Springer Berlin Heidelberg, pp. 253–283. doi:10.1007/3-540-26641-0_12.Google Scholar
Allen, M. J., Hud, N. V, Balooch, M., et al. (1992) ‘Tip-radius-induced artifacts in AFM images of protamine-complexed DNA fibers’, Ultramicroscopy, 42, pp. 1095–1100. doi:http://dx.doi.org/10.1016/0304-3991(92)90408-C.Google Scholar
Baró, A. M. and Reifenberger, R. G. (eds) (2012) Atomic Force Microscopy in Liquid: Biological Applications. Weinheim: Wiley-VCH Verlag GmbH & Co. KGaA.Google Scholar
Bell, G. I. (1978) ‘Models for the Specific Adhesion of Cells to Cells’, Science, 200(4342), pp. 618–627.Google Scholar
Bhushan, B. and Fuchs, H. (2008) Applied Scanning Probe Methods XIII: Biomimetics and Industrial Applications. Berlin, Heidelberg: Springer Berlin Heidelberg (NanoScience and Technology).Google Scholar
Binnig, G., Quate, C. F. and Gerber, C. (1986) ‘Atomic force microscope’, Physical Review Letters, 56(9), pp. 930–933.Google Scholar
Binnig, G., Rohrer, H., Gerber, C. and Weibel, E. (1982a) ‘Surface studies by scanning tunneling microscopy’, Physical Review Letters, 49(1), pp. 57–61.Google Scholar
Binnig, G., Rohrer, H., Gerber, C. and Weibel, E. (1982b) ‘Tunneling through a controllable vacuum gap’, Applied Physics Letters, 40(2), pp. 178–180. doi:10.1063/1.92999.Google Scholar
Bracco, J. N., Stack, A. G. and Higgins, S. R. (2014) ‘Magnesite step growth rates as a function of the aqueous magnesium: carbonate ratio’, Crystal Growth & Design, 14(11), pp. 6033–6040. doi:10.1021/cg501203g.Google Scholar
Busch, H. (1926) ‘Berechnung der Bahn von Kathodenstrahlen im axialsymmetrischen elektromagnetischen Felde’, Annalen der Physik, 386(25), pp. 974–993. doi:10.1002/andp.19263862507.Google Scholar
Calabri, L., Pugno, N., Menozzi, C. and Valeri, S. (2008) ‘AFM nanoindentation: tip shape and tip radius of curvature effect on the hardness measurement’, Journal of Physics: Condensed Matter, 20(47), p. 474208.Google Scholar
Canale, C., Torre, B., Ricci, D. and Braga, P. C. (2011) ‘Recognizing and Avoiding Artifacts in Atomic Force Microscopy Imaging’, in Braga, P. C. and Ricci, D. (eds) Atomic Force Microscopy in Biomedical Research: Methods and Protocols. New York, Dordrecht, Heidelberg, London: Humana Press (Springer Science+Business Media), Methods in Molecular Biology, 736, pp. 31–43. doi:10.1007/978-1-61779-105-5_3.Google Scholar
Chen, C.-L., Qi, J., Tao, J., Zuckermann, R. N. and DeYoreo, J. J. (2014) ‘Tuning calcite morphology and growth acceleration by a rational design of highly stable protein-mimetics’, Scientific Reports, 4, p. 6266.Google Scholar
Dazzi, A. and Prater, C. B. (2017) ‘AFM-IR: technology and applications in nanoscale infrared spectroscopy and chemical imaging’, Chemical Reviews, 117(7), pp. 5146–5173. doi:10.1021/acs.chemrev.6b00448.Google Scholar
Dudko, O. K., Hummer, G. and Szabo, A. (2006) ‘Intrinsic rates and activation free energies from single-molecule pulling experiments’, Physical Review Letters, 96(10), p. 108101.Google Scholar
Edwards, H., Taylor, L., Duncan, W. and Melmed, A. J. (1997) ‘Fast, high-resolution atomic force microscopy using a quartz tuning fork as actuator and sensor’, Journal of Applied Physics, 82(3), pp. 980–984. doi:10.1063/1.365936.Google Scholar
Elhadj, S., De Yoreo, J. J., Hoyer, J. R. and Dove, P. M. (2006) ‘Role of molecular charge and hydrophilicity in regulating the kinetics of crystal growth’, Proceedings of the National Academy of Sciences, 103(51), pp. 19237–19242. doi:10.1073/pnas.0605748103.Google Scholar
Engler, A. J., Rehfeldt, F., Sen, S. and Discher, D. E. (2007) ‘Microtissue Elasticity: Measurements by Atomic Force Microscopy and Its Influence on Cell Differentiation’, in Wang, Y.-L. and Discher, D.E. (eds) Cell Mechanics. London, San Diego, CA: Academic Press, Methods in Cell Biology, 83, pp. 521–545. doi:https://doi.org/10.1016/S0091-679X(07)83022-6.Google Scholar
Enoch, J. M. and Lakshminarayanan, V. (2000) ‘Duplication of unique optical effects of ancient Egyptian lenses from the IV/V Dynasties: lenses fabricated ca 2620–2400 BC or roughly 4600 years ago’, Ophthalmic and Physiological Optics, 20(2), pp. 126–130. doi:10.1046/j.1475-1313.2000.00496.x.Google Scholar
Evans, E. (2001) ‘Probing the relation between force–lifetime–and chemistry in single molecular bonds’, Annual Review of Biophysics and Biomolecular Structure, 30(1), pp. 105–128. doi:10.1146/annurev.biophys.30.1.105.Google Scholar
Evans, E. and Ritchie, K. (1997) ‘Dynamic strength of molecular adhesion bonds’, Biophysical Journal, 72(4), pp. 1541–1555.Google Scholar
Florin, E., Radmacher, M., Fleck, B. and Gaub, H. E. (1994) ‘Atomic force microscope with magnetic force modulation’, Review of Scientific Instruments, 65(3), pp. 639–643. doi:10.1063/1.1145130.Google Scholar
Fortier, H., Vanola, F., Wang, C., and Zou, S. (2016) ‘AFM force indentation analysis on leukemia cells’, Analytical Methods, 8, 4421–4431. doi:10.1039/C6AY00131A.Google Scholar
Friddle, R. (2014) ‘Direct Measurement of Interaction Forces and Energies with Proximal Probes’, in Gower, L.B. and DiMasi, E. (eds) Biomineralization Sourcebook: Characterization of Biominerals and Biomimetic Materials. Boca Raton, FL: CRC Press, pp. 307–318. doi:10.1201/b16621-24.Google Scholar
Friddle, R. W., Noy, A. and De Yoreo, J. J. (2012) ‘Interpreting the widespread nonlinear force spectra of intermolecular bonds’, Proceedings of the National Academy of Sciences, 109(34), pp. 13573–13578. doi:10.1073/pnas.1202946109.CrossRefGoogle ScholarPubMed
Friddle, R. W., Weaver, M. L., Qiu, S. R., et al. (2010) ‘Subnanometer atomic force microscopy of peptide–mineral interactions links clustering and competition to acceleration and catastrophe’, Proceedings of the National Academy of Sciences, 107(1), pp. 11–15. doi:10.1073/pnas.0908205107.CrossRefGoogle ScholarPubMed
Gest, H. (2004) ‘The discovery of microorganisms by Robert Hooke and Antoni van Leeuwenhoek, Fellows of The Royal Society’, Notes and Records of the Royal Society of London, 58(2), p. 187 LP-201.Google Scholar
Girard, P. (2001) ‘Electrostatic force microscopy: principles and some applications to semiconductors’, Nanotechnology, 12(4), p. 485.Google Scholar
Giuffre, A. J., Hamm, L. M., Han, N., De Yoreo, J. J. and Dove, P. M. (2013) ‘Polysaccharide chemistry regulates kinetics of calcite nucleation through competition of interfacial energies’, Proceedings of the National Academy of Sciences, 110(23), pp. 9261–9266. doi:10.1073/pnas.1222162110.Google Scholar
Habibullah, , Pota, H. R., Petersen, I. R. and Rana, M. S. (2013) ‘Creep, hysteresis, and cross-coupling reduction in the high-precision positioning of the piezoelectric scanner stage of an atomic force microscope’, IEEE Transactions on Nanotechnology, 12(6), pp. 1125–1134. doi:10.1109/TNANO.2013.2280793.Google Scholar
Hamm, L. M., Giuffre, A. J., Han, N., et al. (2014) ‘Reconciling disparate views of template-directed nucleation through measurement of calcite nucleation kinetics and binding energies’, Proceedings of the National Academy of Sciences, 111(4), pp. 1304–1309. doi:10.1073/pnas.1312369111.Google Scholar
Higgins, M. J., Proksch, R., Sader, J. E., et al. (2006) ‘Noninvasive determination of optical lever sensitivity in atomic force microscopy’, Review of Scientific Instruments, 77(1), p. 13701. doi:10.1063/1.2162455.Google Scholar
Hölscher, H. and Schwarz, U. D. (2007) ‘Theory of amplitude modulation atomic force microscopy with and without Q-Control’, International Journal of Non-Linear Mechanics, 42(4), pp. 608–625. doi:http://dx.doi.org/10.1016/j.ijnonlinmec.2007.01.018.Google Scholar
Hooke, R. (1665) Micrographia, or, Some physiological descriptions of minute bodies made by magnifying glasses: with observations and inquiries thereupon. London: Royal Society of London.Google Scholar
Huang, Q., Wu, H., Cai, P., Fein, J. B. and Chen, W. (2015) ‘Atomic force microscopy measurements of bacterial adhesion and biofilm formation onto clay-sized particles’, Scientific Reports, 5, p. 16857.Google Scholar
Huckabay, H. A., Armendariz, K. P., Newhart, W. H., Wildgen, S. M. and Dunn, R. C. (2013) ‘Near-field scanning optical microscopy for high-resolution membrane studies’, Methods in Molecular Biology, 950, pp. 373–394. doi:10.1007/978-1-62703-137-0_21.Google Scholar
Hutter, J. L. and Bechhoefer, J. (1993) ‘Calibration of atomic‐force microscope tips’, Review of Scientific Instruments, 64(7), pp. 1868–1873. doi:10.1063/1.1143970.Google Scholar
Jarvis, S. P., Sader, J. E. and Fukuma, T. (2008) ‘Frequency Modulation Atomic Force Microscopy in Liquids’, in Bhushan, B., Fuchs, H., and Tomitori, M. (eds) Applied Scanning Probe Methods VIII: Scanning Probe Microscopy Techniques. Berlin, Heidelberg: Springer Berlin Heidelberg, pp. 315–350. doi:10.1007/978-3-540-74080-3_9.Google Scholar
Knoll, M. and Ruska, E. (1932) ‘Das Elektronenmikroskop’, Zeitschrift für Physik, 78(5), pp. 318–339. doi:10.1007/BF01342199.Google Scholar
Kocun, M., Labuda, A., Gannepalli, A. and Proksch, R. (2015) ‘Contact resonance atomic force microscopy imaging in air and water using photothermal excitation’, Review of Scientific Instruments, 86(8), p. 83706. doi:10.1063/1.4928105.Google Scholar
Kumar, N., Mignuzzi, S., Su, W. and Roy, D. (2015) ‘Tip-enhanced Raman spectroscopy: principles and applications’, EPJ Techniques and Instrumentation, 2(1), p. 9. doi:10.1140/epjti/s40485-015-0019-5.Google Scholar
Labuda, A., Cleveland, J., Geisse, N. A., et al. (2014) ‘Photothermal excitation for improved cantilever drive performance in tapping mode atomic force microscopy’, Microscopy and Analysis, 28(3), pp. S21–S25.Google Scholar
Labuda, A., Kobayashi, K., Kiracofe, D., et al. (2011) ‘Comparison of photothermal and piezoacoustic excitation methods for frequency and phase modulation atomic force microscopy in liquid environments’, AIP Advances, 1(2), p. 22136. doi:10.1063/1.3601872.CrossRefGoogle Scholar
Lekka, M. (2016) ‘Discrimination between normal and cancerous cells using AFM’, Bionanoscience, 6, pp. 65–80. doi:10.1007/s12668-016-0191-3.Google Scholar
Lévy, R. and Maaloum, M. (2002) ‘Measuring the spring constant of atomic force microscope cantilevers: thermal fluctuations and other methods’, Nanotechnology, 13(1), p. 33.Google Scholar
Malotky, D. L. and Chaudhury, M. K. (2001) ‘Investigation of capillary forces using atomic force microscopy’, Langmuir, 17(25), pp. 7823–7829. doi:10.1021/la0107796.Google Scholar
Marsh, G. and Waugh, R. E. (2013) ‘Quantifying the mechanical properties of the endothelial glycocalyx with atomic force microscopy’, Journal of Visualized Experiments, (72), p. e50163. doi:doi:10.3791/50163.Google Scholar
Méndez-Vilas, A., González-Martı́n, M. L. and Nuevo, M. J. (2002) ‘Optical interference artifacts in contact atomic force microscopy images’, Ultramicroscopy, 92(3), pp. 243–250. doi:http://dx.doi.org/10.1016/S0304-3991(02)00140-7.Google Scholar
Mohr, P. J., Newell, D. B. and Taylor, B. N. (2014) ‘CODATA recommended values of the fundamental physical constants: 2014’, Journal of Physical and Chemical Reference Data, 45, p. 043102. doi:10.1063/1.4954402.Google Scholar
Mokaberi, B. and Requicha, A. A. G. (2008) ‘Compensation of scanner creep and hysteresis for AFM nanomanipulation’, IEEE Transactions on Automation Science and Engineering, 5(2), pp. 197–206. doi:10.1109/TASE.2007.895008.Google Scholar
Moreno-Herrero, F. and Gomez-Herrero, J. (2012) ‘AFM: Basic Concepts’, in Baró, A.M. and Reifenberger, R.G. (eds) Atomic Force Microscopy in Liquid: Biological Applications. Weinheim: Wiley-VCH Verlag GmbH & Co. KGaA, pp. 1–34. doi:10.1002/9783527649808.ch1.Google Scholar
Morita, S. (ed.) (2006) Roadmap of Scanning Probe Microscopy. Berlin, Heidelberg: Springer Berlin Heidelberg (NanoScience and Technology).Google Scholar
Niaz, M. (2009) ‘Wave–Particle Duality: De Broglie, Einstein, and Schrödinger’, in Critical Appraisal of Physical Science as a Human Enterprise: Dynamics of Scientific Progress. Dordrecht: Springer Netherlands, pp. 159–165. doi:10.1007/978-1-4020-9626-6_12.Google Scholar
Noy, A., and Friddle, R. (2013) ‘Practical single molecule force spectroscopy: How to determine fundamental thermodynamic parameters of intermolecular bonds with an atomic force microscope’, Methods, 60, pp. 142–150. doi:https://doi.org/10.1016/j.ymeth.2013.03.014.Google Scholar
Orme, C. A., Noy, A., Wierzbicki, A., et al. (2001) ‘Formation of chiral morphologies through selective binding of amino acids to calcite surface steps’, Nature, 411(6839), pp. 775–779.Google Scholar
Passeri, D., Dong, C., Reggente, M., et al. (2014) ‘Magnetic force microscopy’, Biomatter, 4(1), p. e29507. doi:10.4161/biom.29507.Google Scholar
Plantzos, D. (1997) ‘Crystals and lenses in the Graeco-Roman world’, American Journal of Archaeology, 101(3), pp. 451–464. doi:10.2307/507106.Google Scholar
Porter, J. R. (1976) ‘Antony van Leeuwenhoek: tercentenary of his discovery of bacteria’, Bacteriological Reviews, 40(2), pp. 260–269.Google Scholar
Quercioli, F. (2011) ‘Fundamentals of Optical Microscopy’, in Diaspro, A. (ed.) Optical Fluorescence Microscopy: From the Spectral to the Nano Dimension. Berlin, Heidelberg: Springer Berlin Heidelberg, pp. 1–36. doi:10.1007/978-3-642-15175-0_1.Google Scholar
Rahe, P., Bechstein, R. and Kühnle, A. (2010) ‘Vertical and lateral drift corrections of scanning probe microscopy images’, Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena, 28(3), pp. C4E31–C4E38. doi:10.1116/1.3360909.Google Scholar
Roa, J. J., Oncins, G., Diaz, J., Sanz, F. and Segarra, M. (2011) ‘Calculation of Young’s Modulus value by means of AFM’, Recent Patents on Nanotechnology, pp. 27–36. doi:http://dx.doi.org/10.2174/187221011794474985.Google Scholar
Rogers, B., Manning, L., Sulchek, T. and Adams, J. D. (2004) ‘Improving tapping mode atomic force microscopy with piezoelectric cantilevers’, Ultramicroscopy, 100(3), pp. 267–276. doi:http://dx.doi.org/10.1016/j.ultramic.2004.01.016.CrossRefGoogle ScholarPubMed
Rogers, B., York, D., Whisman, N., et al. (2002) ‘Tapping mode atomic force microscopy in liquid with an insulated piezoelectric microactuator’, Review of Scientific Instruments, 73(9), pp. 3242–3244. doi:10.1063/1.1499532.Google Scholar
Sader, J. E. (1995) ‘Parallel beam approximation for V‐shaped atomic force microscope cantilevers’, Review of Scientific Instruments, 66(9), pp. 4583–4587. doi:10.1063/1.1145292.Google Scholar
Sader, J. E., Chon, J. W. M. and Mulvaney, P. (1999) ‘Calibration of rectangular atomic force microscope cantilevers’, Review of Scientific Instruments, 70(10), pp. 3967–3969. doi:10.1063/1.1150021.Google Scholar
Sader, J. E., Sanelli, J. A., Adamson, B. D., et al. (2012) ‘Spring constant calibration of atomic force microscope cantilevers of arbitrary shape’, Review of Scientific Instruments, 83(10), p. 103705. doi:10.1063/1.4757398.Google Scholar
Schillers, H., Medalsy, I., Hu, S., Slade, A. L. and Shaw, J. E. (2016) ‘PeakForce Tapping resolves individual microvilli on living cells’, Journal of Molecular Recognition, 29(2), pp. 95–101. doi:10.1002/jmr.2510.CrossRefGoogle ScholarPubMed
Shen, J., Zhang, D., Zhang, F.-H. and Gan, Y. (2017) ‘AFM tip-sample convolution effects for cylinder protrusions’, Applied Surface Science, 422, pp. 482–491. doi:https://doi.org/10.1016/j.apsusc.2017.06.053.Google Scholar
Tao, J., Battle, K. C., Pan, H., et al. (2015) ‘Energetic basis for the molecular-scale organization of bone’, Proceedings of the National Academy of Sciences, 112(2), pp. 326–331. doi:10.1073/pnas.1404481112.Google Scholar
Terán Arce, P. F. M., Riera, G. A., Gorostiza, P. and Sanz, F. (2000) ‘Atomic-layer expulsion in nanoindentations on an ionic single crystal’, Applied Physics Letters, 77(6), pp. 839–841. doi:10.1063/1.1306909.Google Scholar
Thomas, G., Burnham, N. A., Camesano, T. A. and Wen, Q. (2013) ‘Measuring the mechanical properties of living cells using atomic force microscopy’, Journal of Visualized Experiments, (76), p. 50497. doi:10.3791/50497.Google Scholar
Thomson, J. J. (1897) ‘XL. Cathode rays’, Philosophical Magazine Series 5, 44(269), pp. 293–316. doi:10.1080/14786449708621070.Google Scholar
Umeda, K-i., Oyabu, N., Kobayashi, K., et al. (2010) ‘High-resolution frequency-modulation atomic force microscopy in liquids using electrostatic excitation method’, Applied Physics Express, 3(6), p. 65205.Google Scholar
Voigtländer, B. (2015) ‘Static Atomic Force Microscopy’, in Scanning Probe Microscopy: Atomic Force Microscopy and Scanning Tunneling Microscopy. Berlin, Heidelberg: Springer Berlin Heidelberg, pp. 177–186. doi:10.1007/978-3-662-45240-0_13.Google Scholar
Wallace, A. F., DeYoreo, J. J. and Dove, P. M. (2009) ‘Kinetics of silica nucleation on carboxyl- and amine-terminated surfaces: insights for biomineralization’, Journal of the American Chemical Society, 131(14), pp. 5244–5250. doi:10.1021/ja809486b.Google Scholar
Zhu, Y., Inada, H., Nakamura, K. and Wall, J. (2009) ‘Imaging single atoms using secondary electrons with an aberration-corrected electron microscope’, Nature Materials, 8(10), pp. 808–812.Google Scholar

Save book to Kindle

To save this book to your Kindle, first ensure coreplatform@cambridge.org is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about saving to your Kindle.

Note you can select to save to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be saved to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

Find out more about the Kindle Personal Document Service.

Available formats
×

Save book to Dropbox

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Dropbox.

Available formats
×

Save book to Google Drive

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Google Drive.

Available formats
×