Scanning Probe Microscopy — Python Notebooks (Google Colab)

This repository contains interactive Python notebooks accompanying the textbook:

Scanning Probe Microscopy — From Fundamentals to Quantitative Nanomechanics and Single-Cell Analysis

The notebooks translate textbook concepts into interactive simulations, parameter exploration, and visualization tools.

Each notebook:

• runs directly in Google Colab
• requires no local installation
• includes concept reminders
• allows interactive parameter exploration

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Part I — Foundations of SPM

Chapter 1 — AFM as a Force Sensor

Concepts:

• Hooke's law in AFM
• Thermal noise of cantilevers
• Force–deflection sensitivity

Outputs:

• Force vs deflection plots
• Thermal noise estimation
• Order-of-magnitude reasoning

Launch notebook

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Chapter 2 — Tip–Sample Interactions

Concepts:

• Lennard–Jones interaction
• Jump-to-contact instability
• Hertz contact mechanics
• JKR and DMT adhesion models
• Tabor parameter

Outputs:

• Force–distance curves
• Pull-off force
• Young’s modulus extraction
• Energy dissipation

Launch notebook

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Chapter 3 — AFM Instrumentation and Detection

Concepts:

• Cantilever force–deflection behaviour
• Optical beam deflection (optical lever)
• Thermal noise of AFM cantilevers
• Sensitivity of optical detection

Outputs:

• Force–deflection simulations
• Optical lever sensitivity analysis
• Thermal noise simulations

Launch notebook

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Chapter 4 — AFM Scanning Simulator (Raster Scan + Feedback Artifacts)

Concepts:

• Raster scanning (fast/slow axis), pixel dwell time
• Feedback bandwidth and tracking error
• Imaging artifacts: lag, edge rounding, overshoot, drift
• Tip-size effects (proxy)

Outputs:

• True surface vs measured image
• Tracking error map
• Interactive “artifact laboratory” via sliders

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Launch notebook

Repository Structure

.
├── CITATION.cff
├── LICENSE
├── README.md
├── binder
│   └── requirements.txt
└── notebooks
    ├── README.md
    ├── part-01-foundations
    │   ├── README.md
    │   ├── ch01_force_sensor
    │   │   ├── README.md
    │   │   └── SPM_Ch01_Notebook01_ForceDeflection_Noise.ipynb
    │   ├── ch02_tip_sample_interactions
    │   │   ├── AFM_Force_Distance_LJ_Hertz_Adhesion.ipynb
    │   │   └── README.md
    │   ├── ch03_afm_instrumentation
    │   │   ├── README.md
    │   │   └── SPM_Ch3_AFM_Instrumentation_Python_Exercises.ipynb
    │   └── ch04_afm_scanning_simulator
    │       ├── README.md
    │       └── SPM_Ch4_AFM_Scanning_Simulator.ipynb
    └── utils
        └── README.md

9 directories, 15 files

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How to use the notebooks

1. Click Open in Colab
2. Run the notebook cells sequentially
3. Modify parameters using sliders
4. Explore how AFM physics responds

The notebooks are designed as interactive companions to the textbook, not as standalone scripts.

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License

MIT License