Quantum and Biological Simulation

Python Library

Simulation of systems involving tree structures

• Matrix models of Quantum Systems,
• Random Walk models of Tissue Morphogenesis,
• Cellular Lineage Simulation and Analysis.

MatrixTree

• A graph is constructed from the tree, and a matrix from the leaves.
• A simple, expressive language is used to add and access elements of the graph.
• The matrix terms are accessed through conventional array slicing, but using tree nodes as specifiers, rather than integers.

Crystal

• A crystal is a large MatrixTree, possibly defined by a border.
• Borders can be defined by cuboid, or a polytope in arbitrary dimensions.

Installation

Development

pip install --upgrade -e . --break-system-packages

Running Tests

Individual Module

python -m doctest $module_path

Run All Tests

Execute ./pytest.