Molecular Dynamics

In molecular dynamics the memory state of a system is modeled as a fluid consisting of a collection of atoms which may have bindings between them to form molecules. A molecule consists of a number of atoms all reachable from one of the atoms by sequences of directed links. A directed link from one atom to another atom exists if the former has a so-called field containing the latter. By means of actions causing a change of state, fields can be added to and withdrawn from atoms, and contents of fields can be modified. Selected atoms can also be brought into focus.

Basic instruction sets

• MPP - Molecular Programming Primitives
• MPPV - MPP with Values
• HMPPV - High-level MPPV
• MSP - Molecular Scripting Primitives
• MSPea - MSP with eval and apply
• MSPio - MSP with simple input and output

Example

In this example we use the basic instruction set MPP to build up a list of atoms in focus x.
The resulting fluid after each step is shown on the right.

We initialize the list by creating a new atom and assigning it to the focus x with the instruction

x = new

We can add an atom the the list inf focus x with the following instructions.

We create a new atom in focus y.

y = new

We add a field f to y

y.+f

And assign the atom in focus x to this field.

y.f = x

Assign the atom in focus y to focus x.

x = y

To add another atom to the list, we repeat the last four instructions.