Examine Molecules


Hydrocarbons consist of carbon (gray) and hydrogen (silver) elements with different relative concentrations accounting for different forms.

Alcohols and Sugars

Adding an oxygen (red) with only one bond available produces an Alcohol. An oxygen (red) with two bonds in a carbon loop produce Sugars.


Acids come to be with both the single bond oxygen (red) and the double bond oxygen (red) on the same carbon.

Amino Acids

Adding a carbon and a nitrogen (blue) to the acid produces the Amino Acids, the basic ingredients to life.

And More


Glycolysis represents the
most basic and primitive
form of ATP production.

Cytric Cycle

The Mitochondrion becomes
an ATP producing factory
through the Cytric Acid Cycle.


Hemoglobin in the blood
carries oxygen from lungs
to the rest of the body.


Protein kinase RNA-activated
PKR protects against
viral infections.


Cell membrane
drug pump

Modelling Energy Levels

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Vibrational Nodes of the Nucleus

Oscillation patterns start as the simple s-level expansion/contraction then the p-level movement on different axis. The d-level vibration nodes are both angled and complex. Each state of a vibrational node can hold two electrons.

Modelling an Element

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From Hydrogen to Calcium

Each element has an arrangment of electrons around a empty shell. Electrons do not feel any force from inside the shell, so are pushed to the outside of the shell. They bind to the shell, when the vibration parameters for that part of the shell, match the electron wave function for that vibration.

Modelling a Gas

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The Ideal Gas Law PV = nRT where
  • P is pressure
  • V is volume
  • n is number of molecules
  • R is the gas constant, and
  • T is absolute temperatures

Boyle's law from 1662, states that at constant temperature for a fixed mass, the absolute pressure and the volume of a gas are inversely proportional. This animation illustrates the normal air we breath at 20°C. Free flowing molecules are travelling an average 2.1 nanometers per picosecond, trapped in a 3D box, 30 x 10 x 7.5 nanometers in size.

Modelling a Liquid

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The Van der Waals Radius
and Molecular Bonding

In 1873, Johannes van der Waals, derived the Van der Waals equation where repulsion between molecules has the effect of excluding neighbors from a certain amount of space around each molecule. This principle together with the bonding between molecules is illustrated with 72 molecules bonded together, trapped in a 3D box, 5 x 3 x 2 nanometers in size.

Build You Own Molecule

You can add or delete elements to a molecule and edit the exact location of the elements.

Get data to input from the protein data bank: http://www.rcsb.org, the main repository of molecular structure files. (alternate format)