PGA - ProGram Algebra

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 By means of actions causing a change of state, fields can be added to and withdrawn from atoms, and contents of fields can be modified.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


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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

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.