Building Carbon Nanotubes Manually with Pattern Editors in SAMSON

Modeling carbon nanotubes (CNTs) manually can be challenging if you don’t want to rely on presets or black-box generators. You might want full control over the structure: the number of repetitions, radius, atomic alignment, or even twist between rings. But constructing these from scratch — ring by ring — can feel tedious without proper tools.

In this post, we show how SAMSON’s Pattern Editors can simplify the manual construction of nanotubes, while still giving you complete flexibility. This is useful for computational nanotechnologists and molecular modelers working with customized nanoscale systems.

Quick Overview

SAMSON provides three Pattern Editors:

  • Linear Pattern Editor (shortcut: L)
  • Circular Pattern Editor (shortcut: W)
  • Curved Pattern Editor (shortcut: Q)

These editors let you replicate atomic structures interactively, arrange them in patterns, and control transformations precisely.

Constructing a Nanotube Step by Step

This workflow walks you through using SAMSON to build a nanotube from the ground up, manually:

  1. Create a molecular ring. Ideally, build a ring of carbon atoms (e.g., 6-membered) and rotate it to align its edges with the plane you want.
  2. Activate the Circular Pattern Editor by pressing W. Use the widget to:
    • Increase the number of instances (e.g., 12) – enough to form a complete ring.
    • Adjust the radius so that the ends of the original ring touch and can bond.
    • Click Accept to finalize the ring structure by merging overlapping atoms.
  3. Align the ring using Edit > Align – for example, to the XY plane to prepare for vertical stacking.
  4. Use the Linear Pattern Editor (L):
    • Duplicate the ring upward along the Z-axis (e.g., by 2 Å between each copy).
    • Set rotational offset between stacked rings if your design calls for a twist.
    • Accept the result to build the tube-shaped structure.
  5. Relax the geometry using structure minimization and optionally add hydrogen atoms as needed.

Visual Example

Interactive tutorial in SAMSON

The above image shows one of the key tutorials that build the intuition behind these operations. If you’re new to ring creation or atomic selection in SAMSON, the interactive tutorials available in the software are a helpful starting point.

Why Build a CNT Manually?

Some researchers prefer to control each ring’s composition and alignment, especially when modeling defects, non-standard nanotube geometries, or heteroatom substitutions. The Pattern Editors help you iterate quickly while keeping full control over the molecular design at each step.

You can also reuse parts of the nanotube in other applications — the modular approach enables this reuse.

Learn More

To dive deeper into the full pattern creation toolkit, visit the full documentation page: SAMSON Pattern Editors Documentation.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.

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