From Graphene Sheets to Nano-Batarangs: A Molecular Modeling Tutorial

Molecular modelers often face the challenge of learning new scripting tools while trying to understand complex atom selection and editing processes. If you’re looking for a practical, engaging way to dive into scripted atom selection and modification, SAMSON’s tutorial on creating Batman’s iconic nano-batarang is the perfect place to start.

Through this tutorial, you’ll get hands-on experience with the Simple Script Extension, a tool in SAMSON that allows users to programmatically select atoms and modify their properties using concise scripting methods. What better way to learn advanced concepts than by creating a graphene-based nano-version of Batman’s batarang?

Why Nano-Batarangs?

The concept of crafting a batarang at the nanoscale serves as a memorable, fun, and clear introduction to scripting functionalities. While this may not yield a cancer-curing molecule, it’s an excellent framework for exploring advanced selection rules, mathematical expressions, and the manipulation of atomic geometries—all integral skills in molecular modeling.

Step-by-Step Guide

Below is a quick overview of what this tutorial covers:

Atom Selection: Learn how to focus on specific atoms based on their attributes (e.g., position, element type, or visibility).
Geometric Modifications: Change atom positions using mathematical formulas, enabling creative reshaping of molecular structures.
Efficiency in Scripting: Use concise code to manage large datasets, like simulating molecular structures or designing nanoscale objects.

For example, here’s a snippet from the tutorial that makes a graphene sheet undulate sinusoidally:

a.z := sin(a.x * π / 12);

1	a.z := sin(a.x * π / 12);

This simple script applies a sinusoidal transformation to the z-coordinates of atoms, creating visually engaging patterns.

Fun Example: Batman’s Nano-Batarang

The highlight of the tutorial is the step-by-step creation of a nano-batarang. By combining logical conditions with geometry, you can reshape a flat graphene sheet into Batman’s iconic emblem. Below is a glimpse of the script:

# Adjust visibility and selection based on geometry
var x := a.x / 2;
var y := a.y / 2;
var iambatman := false;
if ((abs(x) > 3 and y >= 0) or (abs(x) > 4 and y < 0)) {
    if ((x/7)^2 + (y/3)^2 < 1) iambatman := true;
}
if (iambatman) {
    n.selectionFlag := 1;
    a.visibilityFlag := 1;
} else {
    n.selectionFlag := 0;
    a.visibilityFlag := 0;
}

# Adjust visibility and selection based on geometry

var x := a.x / 2;

var y := a.y / 2;

var iambatman := false;

if ((abs(x) > 3 and y >= 0) or (abs(x) > 4 and y < 0)) {

if ((x/7)^2 + (y/3)^2 < 1) iambatman := true;

}

if (iambatman) {

n.selectionFlag := 1;

a.visibilityFlag := 1;

} else {

n.selectionFlag := 0;

a.visibilityFlag := 0;

}

This script demonstrates how to delineate specific regions of your graphene sheet to carve out intricate shapes. For instance, you can create ellipsoidal wings, pointy bat ears, or other design elements.

The completed nano-batarang looks like this:

Beyond Fun Shapes

While creating a nano-batarang is entertaining, this skillset applies to numerous tasks in molecular simulation and visualization. From defining regions in biomolecular structures to modifying materials, the scripting knowledge you gain here can be extended across many domains.

Next Steps

So, if you’re ready to explore the possibilities of molecular scripting, start with SAMSON’s Simple Script tutorial and experiment with crafting your own nanoscale creations. To learn more, visit the official documentation page.

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