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Methods in
Molecular Biology 1886
Nuno C. Santos
Filomena A. Carvalho Editors
Atomic Force
Microscopy
Methods and Protocols
METHODS IN MOLECULAR BIOLOGY
Series Editor
John M. Walker
School of Life and Medical Sciences
University of Hertfordshire
Hatfield, Hertfordshire, AL10 9AB, UK
For further volumes:

http://www.springer.com/series/7651
Atomic Force Microscopy
Methods and Protocols
Edited by
Nuno C. Santos and Filomena A. Carvalho

Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
Editors
Nuno C. Santos Filomena A. Carvalho
Instituto de Medicina Molecular Instituto de Medicina Molecular
Faculdade de Medicina Faculdade de Medicina
Universidade de Lisboa Universidade de Lisboa
Lisbon, Portugal Lisbon, Portugal
ISSN 1064-3745 ISSN 1940-6029 (electronic)

Methods in Molecular Biology
ISBN 978-1-4939-8893-8 ISBN 978-1-4939-8894-5 (eBook)
https://doi.org/10.1007/978-1-4939-8894-5
Library of Congress Control Number: 2018961188
© Springer Science+Business Media, LLC, part of Springer Nature 2019

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Preface
Atomic force microscopy (AFM) has been applied over the last 30 years in a variety of
research fields, including physics, chemistry, engineering, biology, and biomedical sciences.
This work intends to collect some of the most relevant and/or recent experimental
approaches “using atomic force microscopy in Biology and Biomedical Sciences.” Our
overall objective was to provide examples of applications using biological samples, showing
different methods for AFM sample preparation, data acquisition, and processing and some
tips and tricks for optimizing AFM measurements and to avoid problems during them. We
have brought together all these recent advances in the AFM field, expecting that this work
can be a bibliographic reference for researchers on different stages of know-how working
with an AFM in biology, from newcomers with low level of knowledge on the use of this
technique to researchers experienced in AFM but that are starting to work with a particular
new type of sample, methodology, or data treatment process.
For those researchers interested in studying biological samples using AFM, the avail-
ability of a comprehensive source of protocols describing the most recent methodological
advances in this technique is invaluable, as many research publications do not provide such
detailed information and technical notes that are critical to be successful in developing the
experiments. For this reason, we have put together a series of protocols written by a
transdisciplinary group of internationally recognized experts working on developing new
tools for addressing distinct biological questions, therefore providing guidelines for better
performing AFM imaging and force spectroscopy experiments.
The book has 21 chapters, divided into 2 main parts. The first part includes six chapters
addressing the AFM imaging of biological samples; the second part is composed of 15 chap-
ters dedicated to different biological applications and experimental aspects of AFM-based
force spectroscopy measurements.
In Chap. 1, Eaton and Batziou [1] describe different experimental artifacts and technical
issues that an AFM user could face while obtaining AFM images. In this chapter, the authors
describe different types of image artifacts pointing solutions to avoid them. This chapter is
extremely useful to all AFM users, especially to the new ones, whom have little chance of
understanding if something is going wrong with an image. In Chap. 2, Connell et al. explain
different methods to process and quantitatively analyze AFM images of phase-separated
supported lipid bilayers [2]. In Chap. 3, Nasrallah et al. detail the protocol to fabricate
supported lipid bilayers, as well as the main guidelines for successfully using high-speed
AFM imaging [3]. Senapati and Park outline the AFM procedures for imaging membrane
proteins (rhodopsin nanodomains) and to perform their quantitative analysis in Chap. 4 [4].
A detailed description of the methods to prepare and image DNA-protein complexes is
given in Chap. 5 by Pisano and Gilson [5]. The first part of the book ends with Chap. 6, in
which Pi and Cai introduce AFM cell topography, which includes the basic principle of AFM
imaging, basic operation modes, imaging of biological sample, critical tips for cell topogra-
phy and its quantitative imaging, as well as some applications [6].
The second part of the book shows different examples of single-molecule force spec-
troscopy studies and protocols to carry them out. To prepare the samples to perform these
studies, first it is necessary to functionalize the AFM tips and supports for molecular
recognition. Ebner et al., in Chap. 7, describe a set of methods by which a variety of
v
vi Preface
proteins, oligonucleotides, or small molecules can be tethered to silicon (nitride) tips or to

mica [7]. Ligand-receptor recognition can be studied using AFM-based single-molecule
dynamic force spectroscopy. In Chap. 8, Liu et al. describe an example of applying single-
molecule dynamic force spectroscopy to study the binding of epidermal growth factor
(EGF) to its receptor (EGFR), testing the effect of two clinical drugs on this ligand-
receptor interaction [8]. On the same field, Sumbul and Rico, in Chap. 9, provide protocols
precisely explaining how to prepare the samples and analyze and interpret the force spec-
troscopy results in terms of available theories [9]. They also present some molecular
dynamics simulations, focusing on steered molecular dynamics that are being used to
explore the mechanics of biomolecular processes such as unbinding and unfolding, at the
single-molecule level. These authors show the importance of bridging computational tools
with the AFM experimental technique. Chapters 10 and 11 are two examples of the
application of AFM-based force spectroscopy. In Chap. 10, Unsay and Garcı́a-Sáez show
how to study the effect of pore-forming proteins in supported lipid bilayers [10], while in
Chap. 11, Pires et al. set different protocols to study neutrophil extracellular traps using
atomic force microscopy [11].
AFM also provides ideal conditions for nanoscale structural and mechanical characteri-
zation of bacterial and viral surfaces, on their native and physiological conditions. Four
different examples of these studies are described on the next chapters, namely, (a) the
protocols by Oh and Hinterdorfer to study bacterial curli production and adhesion
(Chap. 12) [12], (b) the strategies to probe antimicrobial peptides’ action (also applicable
to other antibiotic agents) put forward by Domingues et al. (Chap. 13) [13], and the studies
of viruses and their protein shells by Guo and Roos [14] and Ortega-Esteban et al. [15]
(Chaps. 14 and 15, respectively). Chapter 15 also explains the combination of AFM and
fluorescence methodologies to monitor genome release from individual viral shells during
mechanical unpacking.
The mechanical properties of biological samples can also be evaluated by AFM, as it
combines precise spatial resolution and high force sensitivity. Examples of how to measure
the elastic properties of biological samples are detailed in Chaps. 16–18. Bouchonville and
Nicolas, in Chap. 16, propose a methodology to treat rigidity measurement data, by fitting
parts of the force-indentation curves that correspond to the linear elastic response of the
material [16]. In Chap. 17, Hermann Schillers presents a standardized nanomechanical
AFM procedure that strongly reduces the variability of results obtained on soft samples,
including living cells, by a reliable method to calibrate AFM cantilevers [17]. AFM-based
measurements and data analysis of mechanical properties of single cancer cells are presented
in Chap. 18 by Lekka and Pabijan [18].
Finally, the last three chapters of this book are dedicated to AFM applications in
medicine. Gomes et al., in Chap. 19, describe the use of molecular recognition force
spectroscopy for the characterization and optimization of targeting nanoparticles toward a
given cell-specific interaction [19]. Chapters 20 and 21 are focused on the biomechanical
characterization and activity assessment of live human cardiomyocytes. Pribyl et al., in
Chap. 20, describe the construction of an AFM-based biosensor setup designed to study
the biomechanical properties of cardiomyocyte clusters [20]. On a related work [21],
Caluori et al. studied the single cardiomyocyte electro-chemo-mechanics during
excitation-contraction coupling (Chap. 21). They explain in detail how to implement such
an in vitro system, which can monitor cardiac electrophysiology, intracellular calcium
dynamics, and single-cell mechanics.
Preface vii
In addition to the protocols themselves, the Notes section of each chapter provides
extremely useful and interesting information about some tips and tricks that are not typically
published in the Methods sections of other standard journal articles.
Acknowledgments
We would like to thank Prof. John M. Walker, our Series Editor at Springer International
Publishing AG (a product of Humana Press), for all the help with the publication of this
volume and for the opportunity to bring together an extraordinary collection of articles.
We also would like to thank Fundação para a Ciência e a Tecnologia, Ministério da
Ciência, Tecnologia e Ensino Superior (FCT-MCTES, Portugal), for their support through
the grants PTDC/BBB-BMD/6307/2014 and PTDC/BBB-BQB/3494/2014.
Finally, we are extremely grateful to all the authors that accepted our challenge, for
taking their time to write these exceptional chapters.
Lisbon, Portugal Nuno C. Santos

Filomena A. Carvalho
References
1. Eaton P, Batziou K (this volume) Artifacts and practical issues in Atomic Force Microscopy. Methods
Mol Biol
2. Connell S, Heath GR, Goodchild JA (this volume) Quantitative analysis of structure and dynamics in
AFM images of lipid membranes. Methods Mol Biol
3. Nasrallah H, Vial A, Pocholle N, Soulier J, Costa L, Godefroy C, Bourillot E, Lesniewska E, Milhiet
P-E (this volume) Imaging artificial membranes using high-speed Atomic Force Microscopy. Methods
Mol Biol
4. Senapati S, Park PS-H (this volume) Investigating the nanodomain organization of rhodopsin in native
membranes by atomic force microscopy. Methods Mol Biol
5. Pisano S, Gilson E (this volume) Analysis of DNA-protein complexes by Atomic Force Microscopy
Imaging: the case of TRF2-telomeric DNA wrapping. Methods Mol Biol
6. Pi J, Cai J (this volume) Cell topography and its quantitative imaging by AFM. Methods Mol Biol
7. Ebner A, Wildling L, Gruber HJ (this volume) Functionalization of AFM tips and supports for
molecular recognition force spectroscopy and recognition imaging. Methods Mol Biol
8. Liu J, Li W, Zhang X, Feng Y, Fang X (this volume) Ligand-receptor binding on cell membrane:
dynamic force spectroscopy applications. Methods Mol Biol
9. Sumbul F, Rico F (this volume) Single molecule force spectroscopy: experiments, analysis and simula-
tions. Methods Mol Biol
10. Unsay JD, Garcı́a-Sáez AJ (this volume) AFM to study pore-forming proteins. Methods Mol Biol
11. Pires RH, Delcea M, Felix SB (this volume) Imaging and manipulation of extracellular traps by atomic
force microscopy. Methods Mol Biol
12. Oh YJ, Hinterdorfer P (this volume) Investigation of bacterial curli production and adhesion using
AFM. Methods Mol Biol
13. Domingues MM, Felı́cio MR, Gonçalves S (this volume) Antimicrobial peptides: effect on bacterial
cells. Methods Mol Biol
14. Guo Y, Roos W (this volume) AFM nanoindentation experiments on proteins shells: a protocol.
Methods Mol Biol
viii Preface
15. Ortega-Esteban A, Martı́n-González N, Moreno-Madrid F, Llauró A, Hernando-Pérez M, San

Martı́n C, de Pablo PJ (this volume) Structural and mechanical characterization of viruses with
AFM. Methods Mol Biol
16. Bouchonville N, Nicolas A (this volume) Quantification of the elastic properties of soft and sticky
materials using AFM. Methods Mol Biol
17. Schillers H (this volume) Measuring the elastic properties of living cells. Methods Mol Biol
18. Lekka M, Pabijan J (this volume) Measuring elastic properties of single cancer cells by AFM. Methods
Mol Biol
19. Gomes CP, Oliveira H, Ebner A, Hinterdorfer P, Pêgo AP (this volume) Molecular recognition force
spectroscopy for probing cell targeted nanoparticles in vitro. Methods Mol Biol
20. Pribyl J, Pešl M, Caluori G, Acimovic I, Jelinkova S, Dvorak P, Skladal P, Rotrekl V (this volume)
Biomechanical characterization of human pluripotent stem cell-derived cardiomyocytes by use of
atomic force microscopy. Methods Mol Biol
21. Caluori G, Raiteri R, Tedesco M (this volume) Simultaneous AFM investigation of the single cardio-
myocyte electro-chemo-mechanics during excitation-contraction coupling. Methods Mol Biol
Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xi
PART I IMAGING
1 Artifacts and Practical Issues in Atomic Force Microscopy. . . . . . . . . . . . . . . . . . . . 3

Peter Eaton and Krystallenia Batziou
2 Quantitative Analysis of Structure and Dynamics in AFM Images
of Lipid Membranes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Simon D. Connell, George R. Heath, and James A. Goodchild
3 Imaging Artificial Membranes Using High-Speed Atomic
Force Microscopy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Hussein Nasrallah, Anthony Vial, Nicolas Pocholle, Jérémy Soulier,
Luca Costa, Cédric Godefroy, Eric Bourillot, Eric Lesniewska,
and Pierre-Emmanuel Milhiet
4 Investigating the Nanodomain Organization of Rhodopsin
in Native Membranes by Atomic Force Microscopy . . . . . . . . . . . . . . . . . . . . . . . . . 61
Subhadip Senapati and Paul S.-H. Park
5 Analysis of DNA–Protein Complexes by Atomic Force Microscopy
Imaging: The Case of TRF2–Telomeric DNA Wrapping . . . . . . . . . . . . . . . . . . . . . 75
Sabrina Pisano and Eric Gilson
6 Cell Topography and Its Quantitative Imaging by AFM . . . . . . . . . . . . . . . . . . . . . 99
Jiang Pi and Jiye Cai
PART II SINGLE-MOLECULE FORCE SPECTROSCOPY
7 Functionalization of AFM Tips and Supports for Molecular

Recognition Force Spectroscopy and Recognition Imaging . . . . . . . . . . . . . . . . . . 117
A. Ebner, L. Wildling, and H. J. Gruber
8 Ligand-Receptor Binding on Cell Membrane: Dynamic
Force Spectroscopy Applications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
Jianli Liu, Wenhui Li, Xuejie Zhang, Yan Feng, and Xiaohong Fang
9 Single-Molecule Force Spectroscopy: Experiments, Analysis,
and Simulations. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
Fidan Sumbul and Felix Rico
10 AFM to Study Pore-Forming Proteins. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
Joseph D. Unsay and Ana J. Garcı́a-Sáez
11 Imaging and Manipulation of Extracellular Traps by Atomic
Force Microscopy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 203
Ricardo H. Pires, Mihaela Delcea, and Stephan B. Felix
ix
x Contents
PART III STUDIES OF BACTERIA AND VIRUS IN AFM
12 Investigation of Bacterial Curli Production and Adhesion

Using AFM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 221
Yoo Jin Oh and Peter Hinterdorfer
13 Antimicrobial Peptides: Effect on Bacterial Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . 233
Marco M. Domingues, Mário R. Felı́cio, and Sonia Gonçalves
14 AFM Nanoindentation Experiments on Protein Shells:
A Protocol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 243
Yukun Guo and Wouter H. Roos
15 Structural and Mechanical Characterization of Viruses
with AFM. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 259
Álvaro Ortega-Esteban, Natália Martı́n-González,
Francisco Moreno-Madrid, Aida Llauro, Mercedes Hernando-Pérez,
Cármen San Martı́n, and Pedro J. de Pablo
PART IV AFM ELASTICITY STUDIES
16 Quantification of the Elastic Properties of Soft and Sticky

Materials Using AFM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 281
Nicolas Bouchonville and Alice Nicolas
17 Measuring the Elastic Properties of Living Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . 291
Hermann Schillers
18 Measuring Elastic Properties of Single Cancer Cells by AFM . . . . . . . . . . . . . . . . . 315
Małgorzata Lekka and Joanna Pabijan
PART V AFM APPLICATIONS IN NANOMEDICINE

19 Molecular Recognition Force Spectroscopy for Probing Cell
Targeted Nanoparticles In Vitro . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 327
Carla P. Gomes, Hugo Oliveira, Andreas Ebner, Peter Hinterdorfer,
and Ana P. Pêgo
20 Biomechanical Characterization of Human Pluripotent Stem
Cell-Derived Cardiomyocytes by Use of Atomic Force Microscopy . . . . . . . . . . . 343
Jan Pribyl, Martin Pešl, Guido Caluori, Ivana Acimovic, Sarka Jelinkova,
Petr Dvorak, Petr Skladal, and Vladimir Rotrekl
21 Simultaneous AFM Investigation of the Single Cardiomyocyte
Electro-Chemo-Mechanics During Excitation-Contraction Coupling . . . . . . . . . 355
Guido Caluori, Roberto Raiteri, and Mariateresa Tedesco
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 369
Contributors
IVANA ACIMOVIC Faculty of Medicine, Department of Biology, Masaryk University, Brno,

Czech Republic
KRYSTALLENIA BATZIOU UCIBIO/REQUIMTE, Departamento de Quı́mica e Bioquı́mica,
Faculdade de Ciências da Universidade do Porto, Porto, Portugal
NICOLAS BOUCHONVILLE University of Grenoble Alps, Grenoble, France; Laboratory of
Technologies of Microelectronics, CNRS, Grenoble, France; CEA-Léti-Minatec, Grenoble,
France
ERIC BOURILLOT ICB UMR CNRS 6303, University of Bourgogne Franche-Comte, Dijon,
France
JIYE CAI Department of Chemistry, Jinan University, Guangzhou, China
GUIDO CALUORI Fakultni Nemocnice u Sv. Anny v Brne (FNUSA), International Clinical
Research Centre (ICRC), Brno, Czech Republic; CEITEC MU, Masaryk University, Brno,
Czech Republic; Department of Informatics, Bioengineering, Robotics, and Systems
Engineering (DIBRIS), Università degli Studi di Genova, Genova, Italy
SIMON D. CONNELL Molecular and Nanoscale Physics Group, School of Physics and
Astronomy, University of Leeds, Leeds, UK; Astbury Centre for Structural Molecular
Biology, University of Leeds, Leeds, UK
LUCA COSTA INSERM, U1054, Montpellier, France; Centre de Biochimie Structurale,
Université de Montpellier, CNRS, UMR 5048, Montpellier, France
PEDRO J. DE PABLO Departamento de Fı́sica de la Materia Condensada, Universidad
Autonoma de Madrid, Madrid, Spain; Solid Condensed Matter Institute IFIMAC,
Universidad Autonoma de Madrid, Madrid, Spain
MIHAELA DELCEA ZIK-HIKE, Center for Innovation and Competence—Humoral
Immune Reactions in Cardiovascular Diseases, University of Greifswald, Greifswald,
Germany; DZHK, German Center for Cardiovascular Research, Greifswald, Germany
MARCO M. DOMINGUES Instituto de Medicina Molecular, Faculdade de Medicina,
Universidade de Lisboa, Lisbon, Portugal
PETR DVORAK Faculty of Medicine, Department of Biology, Masaryk University, Brno,
Czech Republic; ICRC, St. Anne’s University Hospital, Brno, Czech Republic
PETER EATON Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de
Lisboa, Lisbon, Portugal; UCIBIO/REQUIMTE, Departamento de Quı́mica
e Bioquı́mica, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
ANDREAS EBNER Institute of Biophysics, Johannes Kepler University Linz, Linz, Austria
XIAOHONG FANG Key Laboratory of Molecular Nanostructures and Nanotechnology,
Institute of Chemistry, Chinese Academy of Sciences, Beijing, China; University of Chinese
Academy of Sciences, Beijing, China
MÁRIO R. FELÍCIO Instituto de Medicina Molecular, Faculdade de Medicina, Universidade
de Lisboa, Lisbon, Portugal
STEPHAN B. FELIX Department of Internal Medicine B, Cardiology, University of
Greifswald, Greifswald, Germany; DZHK, German Center for Cardiovascular Research,
Greifswald, Germany
YAN FENG Key Laboratory of Molecular Nanostructures and Nanotechnology, Institute of
Chemistry, Chinese Academy of Sciences, Beijing, China
xi
xii Contributors
ANA J. GARCÍA-SÁEZ Interfaculty Institute of Biochemistry, University of Tübingen,

Tübingen, Germany
ERIC GILSON Université Côte d’Azur, CNRS UMR 7284/INSERM U108, Institute for
Research on Cancer and Aging, Nice (IRCAN), Medical School, Nice, France;
International Laboratory in Hematology and Cancer, Pôle Sino-Français de Recherche en
Sciences du Vivant et Génomique, Shanghai Ruijin Hospital, Shanghai Jiao Tong
University School of Medicine/Ruijin Hospital/CNRS/INSERM/Nice University,
Shanghai, China; Department of Genetics, CHU Nice, Université Côte d’Azur, Nice,
France
CÉDRIC GODEFROY INSERM, U1054, Montpellier, France; Centre de Biochimie
Structurale, Université de Montpellier, CNRS, UMR 5048, Montpellier, France
CARLA P. GOMES Instituto de Engenharia Biomédica (INEB), Universidade do Porto,
Porto, Portugal; Instituto de Investigação e Inovação em Saúde (i3S), Universidade do
Porto, Porto, Portugal; Faculdade de Engenharia, Universidade do Porto, Porto, Portugal;
Faculdade de Medicina, Instituto de Medicina Molecular, Universidade de Lisboa, Lisbon,
Portugal
SÓNIA GONÇALVES Instituto de Medicina Molecular, Faculdade de Medicina, Universidade
de Lisboa, Lisbon, Portugal
JAMES A. GOODCHILD Molecular and Nanoscale Physics Group, School of Physics and
Astronomy, University of Leeds, Leeds, UK
H. J. GRUBER Institute of Biophysics, Johannes Kepler University Linz, Linz, Austria
YUKUN GUO Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen,
Groningen, The Netherlands
GEORGE R. HEATH Molecular and Nanoscale Physics Group, School of Physics and
Astronomy, University of Leeds, Leeds, UK; Faculty of Biological Sciences, University of
Leeds, Leeds, UK
MERCEDES HERNANDO-PÉREZ Department of Structure of Macromolecules, Centro
Nacional de Biotecnologı́a (CNB–CSIC), Madrid, Spain
PETER HINTERDORFER Institute of Biophysics, Johannes Kepler University Linz, Linz,
Austria
SARKA JELINKOVA Faculty of Medicine, Department of Biology, Masaryk University, Brno,
Czech Republic
MAŁGORZATA LEKKA Department of Biophysical Microstructures, Institute of Nuclear
Physics, Polish Academy of Sciences, Krakow, Poland
ERIC LESNIEWSKA ICB UMR CNRS 6303, University of Bourgogne Franche-Comte, Dijon,
France
WENHUI LI Key Laboratory of Molecular Nanostructures and Nanotechnology, Institute of
Chemistry, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of
Sciences, Beijing, China
JIANLI LIU Key Laboratory of Molecular Nanostructures and Nanotechnology, Institute of
Chemistry, Chinese Academy of Sciences, Beijing, China
AIDA LLAURÓ School of Medicine, University of Washington, Seattle, WA, USA
NATÁLIA MARTÍN-GONZÁLEZ Departamento de Fı́sica de la Materia Condensada,
PIERRE-EMMANUEL MILHIET INSERM, U1054, Montpellier, France; Centre de Biochimie
FRANCISCO MORENO-MADRID Departamento de Fı́sica de la Materia Condensada,
Contributors xiii
HUSSEIN NASRALLAH INSERM, U1054, Montpellier, France; Centre de Biochimie

ALICE NICOLAS University of Grenoble Alps, Grenoble, France; Laboratory of Technologies of
Microelectronics, CNRS, Grenoble, France; CEA-Léti-Minatec, Grenoble, France
YOO JIN OH Institute of Biophysics, Johannes Kepler University Linz, Linz, Austria
HUGO OLIVEIRA Tissue Bioengineering, University of Bordeaux, U1026, Bordeaux, France;
Tissue Bioengineering, INSERM, U1026, Bordeaux, France
ÁLVARO ORTEGA-ESTEBAN Department of Structure of Macromolecules, Centro Nacional de
Biotecnologı́a (CNB–CSIC), Madrid, Spain
ANA P. PÊGO Instituto de Engenharia Biomédica (INEB), Universidade do Porto, Porto,
Portugal; Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto,
Porto, Portugal; Faculdade de Engenharia, Universidade do Porto, Porto, Portugal;
Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto,
Portugal
JOANNA PABIJAN Department of Biophysical Microstructures, Institute of Nuclear Physics,
Polish Academy of Sciences, Krakow, Poland
PAUL S.-H. PARK Department of Ophthalmology and Visual Sciences, Case Western Reserve
University, Cleveland, OH, USA
MARTIN PEŠL Faculty of Medicine, Department of Biology, Masaryk University, Brno, Czech
Republic; ICRC, St. Anne’s University Hospital, Brno, Czech Republic; Faculty of
Medicine, First Department of Internal Medicine—Cardioangiology, Masaryk University,
Brno, Czech Republic
JIANG PI State Key Laboratory of Quality Research in Chinese Medicines, Macau University
of Science and Technology, Macau, China
RICARDO H. PIRES ZIK-HIKE, Center for Innovation and Competence—Humoral
Immune Reactions in Cardiovascular Diseases, University of Greifswald, Greifswald,
Germany; Department of Internal Medicine B, Cardiology, University of Greifswald,
Greifswald, Germany; DZHK, German Center for Cardiovascular Research, Greifswald,
Germany
SABRINA PISANO Université Côte d’Azur, CNRS UMR 7284/INSERM U108, Institute for
Research on Cancer and Aging, Nice (IRCAN), Medical School, Nice, France
NICOLAS POCHOLLE ICB UMR CNRS 6303, University of Bourgogne Franche-Comte,
Dijon, France
JAN PRIBYL CEITEC MU, Masaryk University, Brno, Czech Republic
ROBERTO RAITERI Department of Informatics, Bioengineering, Robotics, and Systems
FELIX RICO LAI, Aix-Marseille Université, INSERM UMR_S 1067, CNRS UMR 7333,
Marseille, France
WOUTER H. ROOS Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen,
Groningen, The Netherlands
VLADIMIR ROTREKL Faculty of Medicine, Department of Biology, Masaryk University, Brno,
Czech Republic; ICRC, St. Anne’s University Hospital, Brno, Czech Republic
CÁRMEN SAN MARTÍN Department of Structure of Macromolecules, Centro Nacional de
Biotecnologı́a (CNB–CSIC), Madrid, Spain
HERMANN SCHILLERS Institute of Physiology II, University of Münster, Münster, Germany
SUBHADIP SENAPATI Department of Ophthalmology and Visual Sciences, Case Western
Reserve University, Cleveland, OH, USA
PETR SKLADAL CEITEC MU, Masaryk University, Brno, Czech Republic
xiv Contributors
JÉRÉMY SOULIER INSERM, U1054, Montpellier, France; Centre de Biochimie Structurale,

FIDAN SUMBUL LAI, Aix-Marseille Université, INSERM UMR_S 1067, CNRS UMR
7333, Marseille, France
MARIATERESA TEDESCO Department of Informatics, Bioengineering, Robotics, and Systems
JOSEPH D. UNSAY Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen,
Germany
ANTHONY VIAL INSERM, U1054, Montpellier, France; Centre de Biochimie Structurale,
L. WILDLING Institute of Biophysics, Johannes Kepler University Linz, Linz, Austria
XUEJIE ZHANG Key Laboratory of Molecular Nanostructures and Nanotechnology, Institute
of Chemistry, Chinese Academy of Sciences, Beijing, China
Part I
Imaging
Chapter 1
Artifacts and Practical Issues in Atomic Force Microscopy

Peter Eaton and Krystallenia Batziou
Abstract
As with any other microscopic technique, in atomic force microscopy (AFM), problems can arise. Some of
these happen due to improper use of the microscope by the operator, and some are due to particular
characteristics of the sample. Some occur depending on the type of instrument, or from probe damage.
Some of them are artifacts inherent in the technique. Knowledge of these issues is important for correct data
acquisition and interpretation, and in many cases, training in AFM is inadequate. In this chapter we show
examples of common artifacts in AFM and describe, where possible, how to overcome them. Other practical
issues important for best practice in AFM operation, such as noise reduction and data processing, are also
discussed.
Key words Artifacts, Distortions, Errors, Technique, Imaging, Force spectroscopy
1 Introduction
Without a doubt, atomic force microscopy is an extremely powerful

and useful technique. In the biological field, in particular, it has
proved its worth by enabling experiments impossible by any other
technique. However, like any other method, it has limitations and is
subject to artifacts that can give rise to errors in images and other
measurements. Such artifacts occur in all instrumental techniques.
For instance, in spectroscopy, peak broadening, shifting, and dis-
tortion can be caused by a wide range of factors [1]. Other types of
microscopy are also prone to exhibit various artifacts [2]. Examples
include chromatic aberrations, which occur in both optical and
electronic microscopies due to imperfect lenses [3]. This kind of
problem causes artifacts in the resulting image. The imperfections
in the lenses lead to corresponding imperfections in the probe (the
electronic or optical beam). Similarly with AFM, imperfect probes
lead to imperfect images, and this is the most common artifact seen
in AFM. In AFM, these probe artifacts are troublesome, because
since the probe usually comes into physical contact with the sample,
it can change during scanning, leading to problems in the image.
Nuno C. Santos and Filomena A. Carvalho (eds.), Atomic Force Microscopy: Methods and Protocols, Methods in Molecular Biology,
vol. 1886, https://doi.org/10.1007/978-1-4939-8894-5_1, © Springer Science+Business Media, LLC, part of Springer Nature 2019
3
4 Peter Eaton and Krystallenia Batziou
With other microscope types, the probe being a beam of radiation,

it tends not to be altered by the sample, and thus does not change
during imaging. On the other hand, probe problems in AFM are
easily remedied (by replacing the damaged or contaminated probe
with a new one), while for electronic microscopy it may mean a
lengthy realignment progress, or require an improved microscopy
objective for optical microscopy.
Probably the second-most common category of artifact in
AFM is that of scanner artifacts. An AFM scanner is an amazing
piece of engineering. It allows positioning and motion of the probe
relative to the sample with sub-nanometer accuracy and precision,
but the high effective magnification and sensitivity of the AFM
means small errors in positioning or translation in the scanner can
be glaringly obvious. AFM scanners are subject to a variety of
different artifacts, which depend somewhat on their design as dis-
cussed below. These can often, though not always, be avoided or
mitigated once the user knows what to look for.
A variety of other artifacts can also occur, some only detected
when making certain kinds of measurements, and some that can be
inadvertently introduced during imaging processing. In general,
most artifacts can be corrected or avoided by the careful user, but
the first step in this process is knowing how to recognize the
artifacts that can occur. Thus, it is highly recommended that as a
new user begins to generate data with the AFM, they familiarize
themselves with these possible sources of error in order to improve
their data. On the other hand, much of the material discussed in
this chapter has previously discussed in AFM training courses, and
following these discussions, many experienced AFM users have
found that they can reinterpret their data once they have been
acquainted with these effects. Artifact and problem recognitions
should be a fundamental part of instrument training.
2 Types of Artifacts
2.1 Probe Artifacts Probe artifacts come about when the shape of the probe is nonideal.
In AFM, as in many other methods, the data output always depends
on the nature of the probe. The image obtained in any microscope
is a convolution of the probe with the sample. In the case of AFM,
the ideal situation is to have the probe with a tip diameter smaller
than the highest resolution required. The probe should also have a
high aspect ratio, such that the probe can reach to the bottom of
any depression or pits in the sample surface, with the minimum of
contact between the sides of the probe and sides of sample features.
However, this is not always the case. Probe-sample convolution and
the effect of different probe sizes are illustrated in Fig. 1.
Sample feature dilation by the probe is an effect that always
occurs in AFM imaging, and can be minimized, but not totally
Artifacts and Practical Issues in AFM 5
Fig. 1 Illustration of effects of probe dilation on the image formed in AFM. In each
case, the left images show the probe and sample feature, the right the image
formed. The first two images show the effect on a raised feature with a small
probe (a), and then with a large diameter tip (b). The lower two images show the
effects of imaging a depressed feature (a pit) with a small (c) and large diameter
tip (d). Raised features tend to be dilated by the probe, while maintaining
accurate height reproduction. On the other hand, depressed features will
become smaller, both in width and height
removed. As described above, for imaging of raised features—for

example, nanoparticles on a flat surface—dilation occurs in the x–y
axes, but not in z axis. While some effects can make z heights
inaccurate, in general, z measurements are highly accurate in
AFM imaging. Image dilation does not occur in the z axis for
these types of features, although measurements of pits or holes in
samples can be inaccurate. This fact, combined with the fact that
the AFM is much more precise in the z axis compared with the x–y
axes, means that accurate measurements of features are ideally made
in the z axis in AFM. Z axis uncertainty can be controlled by
instrumental noise levels, which are normally on the order of
0.1 nm. On the other hand, errors due to dilation in the x–y
Fig. 2 Images showing the differences between imaging with a sharp (a) versus
a blunt (b) probe. Both images show the same sample (biaxially oriented
polypropylene film, BOPP), imaged with a sharp probe (a) and with a probe of
the same type that had been blunted by prolonged use (b)
plane can be very large (10 nm or more), and are difficult to

evaluate without probe shape characterization.
The images in Fig. 2 show an extreme example of sample
dilation. The figure shows height images of biaxially oriented poly-
propylene (BOPP), a polymeric film that is often used as a probe-
characterization sample [4]. The two images shown were measured
at exactly the same scale, but the height image in Fig. 2a shows
many more fibers, and they appear much finer than in Fig. 2b,
which was measured with a very blunt probe. In this case, the
features are dilated, and many features are not seen as they are
smaller than the resolution obtainable with this probe. A sample
such as this can be useful in diagnosis of imaging problems. An up-
to-date of suppliers of probe characterization samples can be found
on the internet [5]. It is highly recommended that AFM labs
should be equipped with a known probe-tip characterization sam-
ple of some kind, to enable diagnosis of probe-related issues. Sev-
eral other types of sample can be used for this purpose, including
gold colloids, porous aluminum, and thin films with many sharp
spikes [6, 7].
While dilation is almost unavoidable in AFM, ideally, the probe
will have an isotropic shape. That is, it should be approximately
cone-shaped with a spheroid tip. Under these conditions, dilation
will not lead to significant shape changes in most cases. However, if
the probe shape is not isotropic (non-spheroid at the end) any
feature imaged by that probe will lead to a feature in the image
with a distorted shape. All commercial probes, when purchased,
should have a more or less ideal shape. Either probe damage or
probe contaminations can lead to distorted images. Very com-
monly, some small part of the sample will adhere to a tip, and
Fig. 3 Examples of tip artifacts leading to repeating shapes in the height images. The samples were protein
nanoparticles (a and c) and a glass microscope slide coated with in proteins (b). All scale bars represent
500 nm
change its shape, leading to distortions in the images. Tip damage

can also occur due to catastrophic failure of the probe material due
to application of high forces [8]. This effect is different to simple tip
wear, which would normally reduce resolution without changes in
shape of the probe. Such tip wear would lead to greater dilation,
but no significant change in feature shape.
Artifacts that give rise to unusually shaped features in the
images can usually be recognized easily, once the user knows what
to expect. Several examples of images containing such tip artifacts
are illustrated in Fig. 3.
If an image such as those shown in Fig. 3 is obtained, it usually
indicates the probe is either broken or contaminated. If the probe is
contaminated or dirty, it might be possible to clean it, while broken
probes cannot be improved, and must be replaced with a new
probe. Cleaning contaminated probes is possible by several meth-
ods [9–12], although in practice the chance of a successful return to
pristine condition is quite low. The method that is simplest is to find
a soft sample, and perform a nanoindentation experiment, using
the AFM software, applying sufficient force to indent into the
sample. Ideally, this will result in the contaminants being deposited
on the soft sample leaving the probe clean. This has been carried
out with the fibrous polymer film BOPP [4], and also with gold
films [7]. However, there are several issues with this:
1. It is not usually possible to distinguish a broken probe from a
contaminated one.
2. Even with contaminated probes, cleaning might be impossible.
3. Even if the contaminants are removed, the probe will probably
already be somewhat blunted due to use.
Fig. 4 Illustration of a double tip effect. Height image of DNA molecules, where
each molecule has an apparent “twin” caused by contamination of the probe.
The x–y scale of the image is 1.5 1.5 μm, and the image height is 2.0 nm
Overall, in most cases, the best thing to do is to swap to a new

probe. Nevertheless, there are some cases where attempting to
clean the probe is justified.
There are some special cases which are actually variations of this
kind of probe artifact.For example, it is possible to have a good
probe, which is accompanied by a “second probe,” which is mostly
likely made up of some contaminating particle. In this case, one can
get a “double tip” effect, where each image feature is accompanied
by a “twin feature” [13]. An example of a double tip effect is shown
in Fig. 4.
Another related effect can occur when the sample contains
large features of considerably higher aspect ratio than that of the
probe. In this case the user obtains an image containing one or
more features that look just like an AFM probe. While many AFM
probes are rounded at the tip, they are usually pyramidal in shape
beyond the very tip. Thus, the image will typically contain pyrami-
dal features when this occurs. Any image of pyramids occurring in
an AFM image must be analyzed with caution as they are often also
artifacts [14]. Sample features that give rise to this effect cannot be
imaged by the AFM using the probe in question. Use of a higher
aspect ratio probe might overcome the problem to a certain extent.
Diagnosis of this problem can benefit from knowledge of the shape
of the particular probe used. For example, many probes are square
or triangular pyramids, giving rise to images showing these shapes
in place of the true sample features.
Both Figs. 2 and 3 showed examples of dilation of sample
features by the probe, leading to artificially larger features in the
final image. But, as illustrated in Fig. 1, when imaging holes in a
sample, such pores will appear artificially smaller due to convolution
of the probe shape. An example image showing this is included in
Fig. 5.
Fig. 5 Illustration of the effect of imaging holes in a sample surface with a blunt tip. (a) Height image of a
calibration artifact which features an array of square holes imaged with a sharp probe. When the same area is
scanned with a blunt probe (b), the holes in the surface appear artificially smaller
Figure 5b illustrates how the holes in the sample surface

become smaller when imaged with a blunt or broken probe. In
this image, the probe was broken and we can also see repeating
triangular shapes in the sample. It’s worth noting that in this case,
the holes were sufficiently large that the probe reached all the way
to the bottom of the pits. This means that the pits were actually
measured to be the same depth in both images. However, for
smaller holes blunt probes will also reduce the depth of concave
features in the image. This is illustrated schematically in Fig. 1.
2.2 Scanner Artifacts In an AFM, the movement of the probe relative to the sample is
carried by a scanner, which translates a voltage produced by the
control electronics to a nano- or micro-metric movement. In nearly
all cases, these are based on piezoelectric crystals, which expand or
contract depending on the polarity of the voltage applied to them.
Since the coefficient of expansion of commonly used piezoelectric
crystals is commonly on the order of 0.01 nm per volt [15], it is
relatively simple with these devices to produce movements with the
nanometric precision required for an AFM.
An ideal AFM scanner would have a perfectly linear relation
between the voltage applied and the distance traveled in all three
axes, would not have any cross talk between movements in different
axes, would respond instantaneously to changes in voltage, and
would also cease movement immediately that the controlling volt-
age ceases changing.
In general, scanners do not produce such perfect movements,
but suffer from a number of imperfections, which give rise to
specific image artifacts which will be discussed in this section. Not
all AFM scanners are the same, as many different designs are in use,
and some reduce or eliminate some of these artifacts.
Finally, apart from the image artifacts produced by piezoelectric
scanners, it is useful for the AFM operator to be aware that piezo-
electrics are quite sensitive materials. They are fragile, and easily
broken. They can also be depolarized by heat or exposure to water,
which will render them useless. Therefore AFM scanners should be
handled with care, and maintained in a dry, room temperature
environment at all times.
2.2.1 Nonlinearity The first major scanner-related artifact is nonlinearity in the x–y
plane. In general, the response of piezoelectrics to voltage is non-
linear. While there are a number of ways to ameliorate, or reduce
this effect, which will be discussed below, if uncorrected this can
introduce severe distortions in the image. Figure 6 illustrates the
effects of this nonlinearity on an image of an AFM calibration grid,
consisting of square, regularly spaced holes in a flat silicon surface.
The two images in Fig. 6 show the same area of the same sample,
scanned using the same instrument and the same AFM probe. The
height image in Fig. 6a was measured using the raw output from
the scanners to linear voltage ramps. It can be seen that in this case,
the response in the X-axis was extremely nonlinear, while linearity
in the y axis was somewhat better but not perfect. The image shown
in Fig. 6b was linearized using position sensors.
There are a number of ways to remedy or improve the linearity
in AFM scanners:
Fig. 6 Example of distortion in the x–y plane of an AFM image due to nonlinearity in the scanner response. The
two images show the same area of the sample. (a) Height image recorded with hardware linearization
disabled, and (b) height image recorded with hardware linearization (displacement sensors) enabled. Both
images are approximately 74 74 μm in x and y and 235 nm in z (height)
1. Some AFM scanner designs are inherently more linear than

others [15]. For example, flexure scanners are commonly
used in some instruments to improve x–y linearity. These scan-
ners do employ piezoelectrics for movement, but the flexure
design reduces non linearity. There are actually quite a wide
range of AFM scanner designs, each of which will tend to give
different characteristic nonlinearity in the scanner movement,
unless corrected.
2. It is possible to employ software-based correction of nonline-
arity. The success of this approach will depend on the sophisti-
cation of the algorithms used to correct for linearity, and also
on the complexity of the distortions inherent in the particular
scanner design. A downside of this approach is that it makes
scanner calibration more complex, and less likely to give highly
accurate results. Nevertheless, it can give good results, and
many popular commercial AFM systems use this approach,
especially older models.
3. The third method is to use what is known as a closed-loop
scanner design. In addition to piezoelectrics to enable the
motion of the probe relative to the sample, displacement sen-
sors are included in the scanner, to measure how far the scanner
actually moves. This information is fed-back to the scanner, to
ensure it moves the exact distance required. This approach is
very effective, and is probably the best method overall. The
image shown in Fig. 6b was measured with displacement sen-
sors and a closed feedback loop. In Fig. 6a, this feedback loop
was disabled, and the resulting distortion can be seen in the
image. Displacement sensors add some complexity to the scan-
ner and electronics design, and as such can be somewhat more
expensive systems. In addition, in some cases, the displacement
sensor’s sensitivity is not fine enough for optimal performance
of the AFM, so open-loop operation (i.e., with feedback from
the sensors turned off) leads to lower noise levels in the images.
In these cases, it is advisable to turn off closed-loop operation
when high resolution or high sensitivity is required. However,
some modern systems feature displacement sensors with very
low noise such that this is unnecessary. If the user suspects that
XY nonlinearity is causing a distortion in the image, and does
not have the option of software or hardware linearization in
their system, the best option is to image a square grid, and
assess the nonlinearity in each port of the image, to determine
the best part to use for scanning. For example, in Fig. 6, it is
clear that the image in Fig. 6b is more linear than the image in
Fig. 6a. Analysis of such an image can also help to determine
the error level in X–Y measurements. Some software packages
can even use this data to perform post-acquisition correction of
images containing X–Y distortion.
2.2.2 Creep Creep is the phenomenon that occurs in piezoelectrics whereby

after a certain movement is made, the piezoelectric tends to con-
tinue to move, even after the voltage stops changing. The practical
effect of this is distortion at the beginning of an image. For exam-
ple, if the image is measured top-to bottom (in the slow scan axis),
then the top few lines will suffer a distortion (Fig. 7b).
It is very simple to avoid this artifact, even in open-loop opera-
tion, however. The simplest method is to ensure the piezo is placed
in the position at which imaging will begin, and wait for the system
to stabilize (effectively reaching point “S” in the plot on the left of
Fig. 7a. This might take 30 s. An alternative is to begin the imaging
in “2D” mode, i.e., measuring profiles continuously, with the
profile being at the start of the desired scan area. Simply watch
the profile over time—if creep is occurring, the features being
scanned will move. After a while, they should stop moving, and it
is a good time to begin the full “3D” scan. Note that this might not
work well in the case that thermal drift is occurring (see Subheading
2.5—Sample drift for this effect).
In systems that continuously scan top to bottom then bottom
to top (as is the case in several commercial systems), this effect will
be minimized by the second scan. Note, that as this effect only
affects part of the image, the data can be corrected post-acquisition
by simply cropping out the affected area (assuming it can be iden-
tified), although some data will be lost in this process.
Fig. 7 The causes and effects of creep. (a) Schematic illustration what happens when a piezoelectric
transducer has a voltage change applied to it—the movement of the piezoelectric tends to continue even
after the voltage stops changing. At the point marked “S,” the creep has stopped, and the system is stabilized,
and suitable to begin measuring an undistorted image. In (b), the result of this effect on atomic force
microscopy images is illustrated. The distortion at the start of the height image (the distortion is seen at the
top, in this figure) is due to creep. The image (b) is approximately 9.5 9.5 μm in x and y and 380 nm in
z (height).This effect should not occur if closed-loop operation is used
2.2.3 Hysteresis (Edge Another effect caused by imperfections in piezo responses is hyster-
Overshoot) esis. Hysteresis in any material is the tendency to fail to return
perfectly to its original shape after extension or compression. In
the piezo actuator in an AFM, this means that in the x–y axis,
forward and back images may be slightly misaligned, although
this is not an important effect for most measurements. Hysteresis
in the z piezo is more important, since it can lead to inaccuracies in
some height measurements, and also in force-distance curve mea-
surements. Examples of the effects of this phenomenon are shown
in Fig. 8.
If the scanner is prone to this effect, it is actually hard to avoid.
The extent of its effects on the image can be lessened somewhat by
scanning more slowly, but will not disappear. The best way to avoid
it, if possible, is to use z sensor height data instead of raw height
data. This is only available if the instrument in use has a displace-
ment sensor on the z piezo. Use of the z sensor data will also
improve the accuracy of force-distance curves. In both cases, it’s
worth bearing in mind that if the z sensor has a considerable noise
level, using this data instead of the standard z height data may result
in better accuracy but lower precision.
Fig. 8 Effects of hysteresis in piezo actuators in AFM. (a) The image is from a height measurement over
square-profile posts that shows where errors can occur when passing over steep features. (b) An example of
an uncorrected deflection-distance curve (from which force-distance curves are calculated. Close to the
turnaround point at the right (arrowed), the forward and back traces do not match due to piezo hysteresis
2.2.4 Scanner Calibration All AFM systems require calibration of the scanner movement in
order to deliver quantitative results. Commercial systems should be
delivered with an accurate calibration, and a certification indicating
the error in the calibration measurement. Nevertheless, piezoelec-
tric materials age over time, which means that, the exact number of
nanometers they move per applied volt changes. Typically, this
change is faster at the beginning of a scanner’s lifetime, and stabi-
lizes over time. It is highly recommended that the scanner is cali-
brated against a trusted calibration artifact 6 months after
installation, and every year thereafter. Calibration procedures have
been extensively described elsewhere [16].
2.3 Noise Vibrations in the AFM system inevitably give rise to noise in the
data produced. This is common in all high-resolution microscopes.
2.3.1 Acoustic
In AFM, compared to electronic microscopes, the system can be
and Mechanical Noise
more troublesome for two reasons. Firstly, the AFM is often a small
system, so it’s more prone to mechanical vibration. Secondly, in
AFM, the probe physically touches the sample, forming a mechani-
cal loop, which transmits all vibrations in the system into the probe-
sample interface. Typically, AFM installations include some form of
vibration isolation, which reduces these effects to an acceptable
level. Acoustic isolation might be included as well. Nevertheless,
these measures only reduce the level of noise. Figure 9 shows image
recorded in an AFM system located in a fully working vibration, and
acoustic enclosure. In Fig. 9, parts A and B are images recorded in
quiet conditions. Figure 9 (parts c and d) are similar images
recorded with people in the room talking and performing various
noisy activities. These produce significant transient noise in the
image.
In Fig. 9, the noise is clearly visible in the lower right hand error
image (Fig. 9d), and somewhat harder to perceive in the
corresponding height image, at the top right (Fig. 9c). But height
images do contain marked vibrations. These are illustrated in the
height profiles in Fig. 10, which were extracted from the images a
and c from Fig. 9.
In order to avoid the problems shown in Fig. 9, it is important,
firstly, to ensure the AFM instrument is shielded toward both
acoustic and vibrational influences. There are many commercial
vibration solutions available, both active and passive. Passive solu-
tions generally work by connecting the AFM instrument to a large
mass on the end of a soft spring. In this way, high frequency
vibrations are absorbed by the mass-spring system. Active systems,
on the other hand, use accelerometers to measure vibrations com-
ing into the system, and actively compensate for these using actua-
tors. Either kind of system can work extremely well to reduce (but
not to eliminate) vibrations entering the AFM system. Thus it’s
important to install the AFM in a low-noise environment, and avoid
the kind of transient impulses illustrated in Fig. 9. Acoustic
Fig. 9 Examples of transient noise effects in AFM images. All images show the same area of an HOPG sample.
(a, b) show height and amplitude images, respectively, of the samples taken under quiet conditions, i.e., with
the AFM enclosed in a vibration isolation cabinet, and no acoustic or vibration sources in the room. (c, d) show
the equivalent images of the same area with talking and noisy activities occurring in the room. The lines
marked P1 and P2 refer to profiles through these images shown in Fig. 10
Fig. 10 Height profiles indicating interference in height profiles from acoustic and vibrational noise. The graphs
show two line profiles (P1, P2) from Fig. 9a, c. In both graphs, the blue solid line shows the height profile
measured during noisy conditions (from Fig. 9c), while the red dashed line shows the same line recorded
under quiet conditions (from Fig. 9a)
shielding can be sufficient to effectively reduce low-amplitude

noises, such as talking, and can be constructed fairly simply, typi-
cally consisting of a wooden box with foam on the inside. Measure-
ment of the noise floor of the AFM is typically used to assess the
success of vibration and acoustic noise reduction. The method to
measure noise floor has been discussed elsewhere [11]. AFM
instruments benefit from being installed on lower floors, away
from foot traffic and heavy machinery to reduce noise.
2.3.2 Electronic Noise It is possible for the AFM to pick up electronic noise from the
surrounding environment (e.g., radio-frequency interference), or
from an internal fault in the AFM to give rise to electronic noise in
the image. External noise sources can be diagnosed by switching off
possibly interfering devices. Fluorescent lights are a common cul-
prit in this regard, either malfunctioning, or not. Internal problems
in the AFM may be harder to deal with, but it’s important that the
user check for loose wires if such a problem is suspected. Very
commonly such problems are simple to diagnose, since they are
either completely constant, or switch on and off suddenly, unlike
other sources of noise, and have fixed frequencies. Commonly, this
will be the frequency of the mains AC source (i.e., either 50 or
60 Hz), which can be measured in the AFM image (Fig. 11).
2.3.3 Bit Noise “Bit noise” is an effect due to the limited bit resolution in the
analogue to digital converters (ADCs) which are a vital part of the
AFM. Usually this is only seen in z height images, when looking at
extremely flat samples, or measuring very small images. It comes
about because the AFM electronics usually record the height data
as 16-bit numbers. With 16 bits, the number of discrete height
values that can be registered is 216, i.e., 65,536. While this is a very
large number, and is sufficient for most cases, since the AFM is
extremely sensitive in z, it can be a limitation. If we take the case of
a very large scanner, with 10 μm height range, we can determine
that the smallest value that can be distinguished is 10,000/
65,536, i.e., 0.15 nm. This is a pretty small measurement, espe-
cially in a range of 10 μm; however, most AFMs will have a noise
floor several times smaller than this value. Thus for high-resolu-
tion imaging, bit noise can be a significant factor in image quality.
Fortunately, it is a limitation which is generally easy to overcome.
One solution is to use a smaller scanner. AFM instruments are
often purchased with multiple scanners for imaging samples with
difference size features. This does work, but it’s an expensive
solution to a simple problem with a simple solution. With most
systems, it’s possible to artificially limit the range of the scanner
used when imaging under high-resolution/low-noise conditions.
This has the effect of greatly reducing the bit noise. For example,
in the case above, the same scanner might be used with the
effective range of only 1 μm. Thus, the sampling would occur at
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Title: History of the United Co-operative Baking Society Ltd

A fifty years' record 1869–1919
Author: William Reid
Release date: September 28, 2023 [eBook #71749]
Language: English
Original publication: United Kingdom: United Co-operative Baking

Society Limited, 1920
Credits: Richard Tonsing, MFR, and the Online Distributed

Proofreading Team at https://www.pgdp.net (This file was
produced from images generously made available by The
Internet Archive)
*** START OF THE PROJECT GUTENBERG EBOOK HISTORY OF

THE UNITED CO-OPERATIVE BAKING SOCIETY LTD ***
Transcriber’s Note:
New original cover art included with this eBook is
granted to the public domain.
CENTRAL PREMISES
HISTORY
OF THE
UNITED CO-OPERATIVE BAKING SOCIETY

LTD.
A FIFTY YEARS’ RECORD
1869–1919
BY WILLIAM REID
Published by United Co-operative Baking Society Limited

M‘Neil Street, Glasgow
1920
PREFACE.
The chief advantage of prefaces is the opportunities they give

authors for making apologies and for returning thanks. In the
present instance the hurry with which the book has had to be written
did not allow time enough to do many things which the writer would
have liked to do. He would have liked to linger with the old-time
enthusiasts who laid the foundations of the Society, to have made
himself as familiar as possible with the times in which they lived and
with the thoughts in their minds, so that he might be able to present
to his readers a picture of their times as they saw them, and of their
difficulties as they had to encounter them. For this there was no
time, and so he has had to content himself with telling a plain,
unvarnished tale of difficulties met and overcome, of a faith which
refused to be dismayed, and of a triumph which is visible to all.
Unfortunately, there is no one alive to-day who had any active part
in the inception of the Society. This increased the difficulty of
presenting a true picture of the beginnings of the Society, but some
help in this direction was got from the “Year Book,” which had been
written by Mr Lochrie in 1896. The writer is also very much indebted
to Mr David Brown, of the office staff of the Society, who prepared
synopses of the various minutes of the Society. These synopses, by
indicating the salient points in the minutes, greatly lightened the
labour of selection; but, in addition, every minute has been carefully
read at least once, and many of them much oftener, so that complete
accuracy might be secured.
Great assistance in dealing with the history of the last thirty years
has also been given by Mr James H. Forsyth, cashier of the Society,
whose knowledge of the transactions of that period is unparalleled.
W. R.
CONTENTS.
CHAP. PAGE
I. Scotland in the Seventeenth and Eighteenth
Centuries 1
II. The Dawn of Co-operation 7
III. The First Year 17
IV. St James Street Bakery 29
V. The Branch Controversy 43
VI. St James Street: Developments 56
VII. St James Street: Congestion 69
VIII. M‘Neil Street 82
IX. M‘Neil Street: Rapid Developments 97
X. Further Developments 110
XI. Further Extensions 123
XII. Continuous Development 144
XIII. Clydebank Branch 158
XIV. Belfast Branch 166
XV. A New President 184
XVI. From Strength to Strength 197
XVII. Progress Continues Steady 210
XVIII. Baking under War Conditions 224
XIX. Bread Baking under Control 238
XX. Educational Work 253
XXI. Men Who Wrought 262
Statistics 273
ILLUSTRATIONS.
Central Premises Frontispiece

Coburg Street and St James Street Premises Facing page 16
M‘Neil Street Premises „ 17
M‘Neil Street Premises „ 32
Clydebank Bakery „ 33
Past Presidents (1) „ 64
Past Presidents (2) „ 65
President and Secretary „ 80
Auditors „ 81
Directors (1) „ 112
Directors (2) „ 113
Belfast Advisory Committee „ 128
Manager and Cashier „ 129
Educational Committee „ 160
Prize Silver Band „ 161
Belfast Bakery „ 176
St Mungo Halls „ 177
Departmental Managers (1) „ 208
Departmental Managers (2) „ 209
Deputations to England (1) „ 224
Deputations to England (2) „ 225
Roll of Honour „ 277
CHAPTER I.
SCOTLAND IN THE SEVENTEENTH AND
EIGHTEENTH CENTURIES.
GENERAL SOCIAL CONDITIONS—EARLY FARMING

METHODS—POVERTY OF THE PEOPLE—MINERS AS
SERFS—“THE SOUTH SEA BUBBLE”—IMPROVING
CONDITIONS: THE ACT OF UNION AND ITS EFFECTS—
THE INDUSTRIAL REVOLUTION—THE FACTORY SYSTEM:
ITS EFFECT ON THE STATUS OF MEN.
The conditions under which the people of Scotland lived during

the seventeenth and eighteenth centuries were rude and uncouth,
and, when judged by modern standards, could scarcely be described
as other than appalling. In the few towns of any size, stone buildings
were the rule; but in the rural districts the majority of the people
lived in huts, the walls of which were built of sods and stones, and
which were roofed with wattles and thatched with rushes. These huts
were windowless save for a hole in the wall which admitted some air
but very little light during the summer, and which was stuffed with
rags and rushes during winter in order to keep out the snell North
wind. The floor was but earth, hardened with the trampling of
countless feet; and fireplace or chimney there was none, unless a few
stones set in the middle of the floor or against one of the gables can
be called a fireplace, and a hole in the roof, through which the smoke
found its way after it had explored every nook and cranny of the
house, a chimney.
Famine was an almost annual visitor. The majority of the people
lived by agriculture, but the land was cold and undrained, and the
methods of tilling were ineffective. The motive power was sometimes
provided by oxen, but often the people harnessed themselves to the
primitive implements. The result was that the grain grown was poor
in quality and scanty in quantity, while often it failed to ripen
because of the wetness of the soil, and because, also, of lateness in
sowing. The cattle were poor and underfed. Roots for feeding
purposes were unknown until near the end of the period; there was
no grain to spare, and little straw or hay for winter feeding, so that
the poor brutes had to forage for themselves as best they could.
In the hall of the laird the position was a little better, but few of the
lairds of that day could aspire to the standard of living of a
moderately well-to-do farmer of to-day. Of food there was always
enough in the hall, but it was coarse and unsavoury. Throughout the
winter fresh meat was unknown. The cattle were killed in the
autumn; the meat was stored in brine barrels, and this brine-soaked
meat, or swine flesh preserved in the same manner, was the only
meat which found a place on the table of the laird during the winter
months, except on the few occasions of great importance when one
or two fowls were killed.
The farming class, if it be not a misnomer to call them farmers,
usually lived in groups of such huts as are described above, and tilled
their land more or less in common. The system chiefly in vogue was
the “run rig” system, under which exchange of ground took place
every year. The more important of their crude implements were also
held in common, and as these could only be used by one person at a
time—as, also, it was often well on in the spring before any thought
of tillage occurred to them or the condition of their water-logged soil
would permit of it, and as much time was often lost in deciding the
rotation in the use of the implements—the return in the good years
was only just sufficient for their wants. As the bad years were
generally twice as numerous as the good years, the conditions of the
rural workers were generally most miserable. Ill-treated Nature,
receiving no encouragement from man save the “tickling of her face
with a stick,” refused to give of her bounty, and the people who
depended on her for life suffered accordingly.
A condition of continual hunger was the lot of the labourers who
had no land to till. They were often forced to depend for food on the
roots and berries they could gather in the woods; the scraps which
went to feed the laird’s pigs were luxuries which only came their way
at long intervals. Work was intermittent; it was poorly paid, for
money was even scarcer than food. The only landless men who had
what might be termed a decent living wage for the period were the
miners. They received about a shilling a day; but, in return, they sold
themselves into serfdom, for, from the beginning of the seventeenth
century until the closing year of the eighteenth, no man, woman, or
child who once entered a mine to work in it could leave it again. If
the mine was sold the sale carried with it the right to their labour;
they were bondslaves until death, the great emancipator, burst their
shackles and set them free for ever.
On the large farms, which became more numerous during the
eighteenth century, ploughmen received the truly magnificent salary
of 35/ a year, with one or two perquisites, of which one was a pair of
boots. The ploughman’s daughter, if she went to the farm to assist
the farmer’s wife and daughters with the cows, received, as a reward
for her labour, 13/4 a year, a piece of coarse cloth for an apron, and a
pair of shoes.
In the towns the conditions were little better. In the early years of
the eighteenth century a succession of bad years brought distress to
all sections of the populace. There was much unrest, which was
fanned into flame by the passing of the Act of Union in 1707, when a
considerable amount of rioting took place in various parts of the
country. In addition, the foreign trade of the country had been
ruined by the English Navigation Act of 1660, which provided that all
trade with the English Colonies should be carried in English ships
alone.
In the closing years of the seventeenth century Paterson, the
founder of the Bank of England, launched his Darien scheme,
famous in history as “The South Sea Bubble,” for the purpose of
inaugurating a great world exchange and mart at the Isthmus of
Panama. Scotsmen became responsible for £400,000 of the capital,
and actually paid in £220,000. The jealousy of the English
merchants, however, together with the fact that it had been proposed
to establish a depot on land which was claimed by Spain, without
having gone through the formality of consulting that country
beforehand, handicapped the scheme from the outset. Nevertheless,
although opposed by the English, and cold-shouldered by the Dutch,
whose help they had hoped to enlist, the Scotsmen persevered with
their project. A company, numbering 1,200, set out for their
destination, landed, and erected a fort. Difficulties came fast,
however. The King had not given his consent to the scheme, and the
American colonists refused to have anything to do with them.
Supplies gave out before the new crops were ready, and none were
forthcoming from home, so that at the end of eight months the
colony was broken up. Out of a total of 2,500 persons who had left
Scotland, not more than thirty ever reached home again. The failure
of the scheme caused untold misery and ruin in Scotland, and did
much to engender the bitter feelings toward the English which
showed themselves when the union of the two Parliaments was being
discussed; but, worst of all, it bled the country white; so much so that
when, a few years later, the British Government called in the Scottish
coinage in order to replace it with coinage of the United Kingdom,
only coinage to the value of £400,000 was returned to Scotland.
IMPROVING CONDITIONS.
The Act of Union was exceedingly unpopular, but, as it turned out,
it was not an unmixed evil, for it placed Scottish traders on the same
footing as the English in respect to trading with the Colonies, from
which they had been debarred for fifty years. It also gave Scottish
ships free entry to English ports and Scottish goods free entry to
English markets, and so marked the beginning of the increasing
prosperity which has come to Scotland since then.
In particular the opening up of trade with the Southern Colonies
had much to do with laying the foundation of the proud commercial
position which Glasgow holds to-day. Merchants from the little town
on the banks of the Clyde began to trade with these Colonies,
bringing back in exchange for their wares tobacco and other
products, including cotton. During the same period there was
introduced from Holland the art of fine spinning, and on these two
articles of Colonial produce—tobacco and cotton—were built up
many fortunes. Later in the century the invention of the spinning
jenny, the carding frame, and the power-loom, and the discovery by
Watt of how to harness the power of steam to production all gave an
impetus to the commercial growth of Scotland. With the application
of the power of steam the foundation of Scotland’s pre-eminent
position in the manufacture of iron and steel and in the building of
ships was laid, for by the application of steam-power to pumping
machinery and to haulage it was found possible to keep her coal pits
free from water and to dig vertical shafts to the coal seams.
Thus the eighteenth century, which had begun with the Scottish
people in the direst poverty, ended with many of them in
comparative comfort and with the standard of living for all definitely
raised. Never since then, not even in the period of deep poverty
which followed the close of the Napoleonic war nor in the “hungry
’forties,” have the whole people fallen back into the depths of misery
in which they were sunk at the beginning and all through the
seventeenth century and well into the “’twenties” of the eighteenth.
At times since then progress seemed to be at a standstill; at times it
seemed even to be on the down grade; but the impetus has always
been recovered; the standard of living has been rising gradually, and
although we are still far removed from the rude profusion which has
caused the century in English history which followed the “Black
Death” to be spoken of as “the golden age of labour,” the trend of our
march is in the direction of a condition which, measured by the
different standards of to-day, will approximate to that long past
happy period.
THE FACTORY SYSTEM.
While it is admitted that the inventions and discoveries of Sir
Joseph Arkwright (partner of David Dale at Lanark), Hargreaves,
Crompton, and Cartwright revolutionised industry, and in the long
run brought a higher standard of living to the people, yet the first
results of their application were not wholly good. For centuries
spinning and weaving had been carried on in the homes of the
people, but with the invention of the spinning jenny, the carding
frame, and the power-loom the weaving industry was removed to
larger buildings. At first these were merely makeshifts. A disused
stable or cowshed, any building, in fact, which would house a
number of looms was good enough for the new industry. The hand-
loom weavers soon found that they were unable to compete with the
new methods. To make matters worse, where they did not
themselves give up and take service under the new regime, their
wives and their children did, and became competitors in driving the
husbands and fathers out of the industry.
Soon the millowners discovered that in the new methods with the
new cheap labour there was a mine of wealth and, their greed
growing by what it fed on, they sought for even cheaper labour than
that of the poorly paid wage-slave women and children. This cheaper
labour they found in the thousands of pauper children under the care
of the supervisors of the poor. The story of the cruel treatment of
these poor little mites, who were often chained to the frames of the
looms and whipped to keep them awake, is one of the blackest pages
in the whole history of the growth of the capitalist system in Great
Britain.
In the weaving trades the entry of women and children changed
the whole economy of the weavers’ homes. Formerly the work had
been done by the male members of the families, assisted to some
extent by the women, but under the new system the factory owner
found that he could get as much work done by the mother at a
considerable reduction on the wages paid to her husband, and so the
husband found himself workless. Then it was found that the children
soon became as expert as their elders, and so a further reduction in
wages took place.
The net result was that it became a case of equal pay for equal
work, but the standard of pay was that of the women and not of the
men, and soon the whole family had to work to provide the
necessaries of life for the home which should have been provided by
the wages of the husband alone. Even to-day, while the women of the
cotton mills who are members of their unions are probably the best
paid female workers in the country, the standard for men is much
below that for male workers in other trades; so that, in the case of the
factory workers, “equal pay for equal work” has meant a general
lowering of the standard of pay.
CHAPTER II.
THE DAWN OF CO-OPERATION.
CO-OPERATION IN PREHISTORIC TIMES—EARLY TEUTONIC

CO-OPERATION—THE SCOTTISH CLAN SYSTEM—THE
PRESENT CO-OPERATIVE SYSTEM—FENWICK AND
OTHER CO-OPERATIVE SOCIETIES—EARLY CO-
OPERATIVE BAKERIES—THE GLASGOW BAKING
SOCIETIES—EARLY METHODS OF CONTROLLING PRICES
—STIRLINGSHIRE AND THE HILLFOOTS—BAKING
SOCIETIES IN FIFE AND THE NORTH—CO-OPERATIVE
BAKING IN THE BORDERLAND—GLASGOW SOCIETY—CO-
OPERATIVE BAKING IN 1866—THE FIRST FEDERATED
BAKERY.
The Co-operative principle is as old as human intelligence. As soon

as man became possessed of the first faint glimmerings of reason he
began to seek communion with his fellows, and began, also, to take
concerted action with them for mutual protection. It was natural that
this should be so. The world must have been a terrible place for the
human race in those early days. On land, in the sea, and in the air it
was peopled with monsters, against whose attacks the unaided
strength and skill of a solitary human were of no avail. Only by
combination could he hope to survive. Results have proven that
combination—Co-operation—is the law of life; that the men, the
animals, the insects even which have learned to combine, have
progressed in the scale of evolution; while the solitary monsters of
past ages have disappeared, and are known only from a bone found
here and a partially complete skeleton there.
That the human race gathered together in communities very early
in its history there is abundance of evidence. In some of our cliffs
there are caves which bear traces of human habitation; while
scattered here and there over the world are immense mounds of
shells, extending sometimes to a depth of many feet and acres in
width, on what is believed to have been the seashore of prehistoric
times, which show that, for a long period, these places were
frequented by communities.
This community living has continued all down the ages. The
“commune” system in vogue amongst the Teutonic races was an
imperfect system of Co-operative farming by an agricultural
community, which finally ceased in Germany during the nineteenth
century. It was introduced into this country by the invading Teuton
races in the early centuries of the Christian era; and, with various
modifications and adaptations, was still in being at the time of the
Norman conquest. From that date it gradually declined, until, by the
end of the sixteenth century, it had all but died out in England, but
was still alive in parts of Scotland in the clan system. There the old
community spirit continued to prevail until after the rebellion of
1745, when the common lands of the clans were given to the chiefs.
In the lowlands, also, some trace of this principle continued to be
visible amongst the farming community.

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Atomic Force Microscopy: Methods and

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ISSN 1064-3745 ISSN 1940-6029 (electronic)

© Springer Science+Business Media, LLC, part of Springer Nature 2019

proteins, oligonucleotides, or small molecules can be tethered to silicon (nitride) tips or to

Lisbon, Portugal Nuno C. Santos

15. Ortega-Esteban A, Martı́n-González N, Moreno-Madrid F, Llauró A, Hernando-Pérez M, San

1 Artifacts and Practical Issues in Atomic Force Microscopy. . . . . . . . . . . . . . . . . . . . 3

PART II SINGLE-MOLECULE FORCE SPECTROSCOPY

7 Functionalization of AFM Tips and Supports for Molecular

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PART IV AFM ELASTICITY STUDIES

16 Quantification of the Elastic Properties of Soft and Sticky

PART V AFM APPLICATIONS IN NANOMEDICINE

IVANA ACIMOVIC  Faculty of Medicine, Department of Biology, Masaryk University, Brno,

ANA J. GARCÍA-SÁEZ  Interfaculty Institute of Biochemistry, University of Tübingen,

HUSSEIN NASRALLAH  INSERM, U1054, Montpellier, France; Centre de Biochimie

JÉRÉMY SOULIER  INSERM, U1054, Montpellier, France; Centre de Biochimie Structurale,

Artifacts and Practical Issues in Atomic Force Microscopy

Key words Artifacts, Distortions, Errors, Technique, Imaging, Force spectroscopy

Without a doubt, atomic force microscopy is an extremely powerful

With other microscope types, the probe being a beam of radiation,

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Figure 5b illustrates how the holes in the sample surface

1. Some AFM scanner designs are inherently more linear than

2.2.2 Creep Creep is the phenomenon that occurs in piezoelectrics whereby

shielding can be sufficient to effectively reduce low-amplitude

Title: History of the United Co-operative Baking Society Ltd

Author: William Reid

Release date: September 28, 2023 [eBook #71749]

Original publication: United Kingdom: United Co-operative Baking

Credits: Richard Tonsing, MFR, and the Online Distributed

*** START OF THE PROJECT GUTENBERG EBOOK HISTORY OF

UNITED CO-OPERATIVE BAKING SOCIETY

Published by United Co-operative Baking Society Limited

The chief advantage of prefaces is the opportunities they give

Central Premises Frontispiece

GENERAL SOCIAL CONDITIONS—EARLY FARMING

The conditions under which the people of Scotland lived during

CO-OPERATION IN PREHISTORIC TIMES—EARLY TEUTONIC

The Co-operative principle is as old as human intelligence. As soon

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