$Revision: 675 $

Copyright © 2011 Johan Elf, David Fange, Johan Hattne, Anel Mahmutovic

Copyright (c) 2004-2011 Johan Elf, David Fange, Johan Hattne, Anel Mahmutovic. Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.2 or any later version published by the Free Software Foundation; with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts. A copy of the license is included in the section entitled "GNU Free Documentation License".

This product includes software developed and copyright by

Makoto Matsumoto and Takuji Nishimura ( http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/emt.html)

Richard J. Wagner ( http://www-personal.umich.edu/~wagnerr/MersenneTwister.html)

and Jasper Bedaux ( http://www.bedaux.net/mtrand)

Roldan Pozo, Karin Remington, and Andrew Lumsdaine. ( http://math.nist.gov/sparselib++/).

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

The names of its contributors may not be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

This product includes software developed by the Apache Software Foundation (http://www.apache.org).

This product includes software developed by Ben Bornstein ( http://www.sbml.org/libsbml.html).

**Table of Contents**

- Welcome to the Wonderful World of MesoRD
- 1. Introduction
- 2. Installation
- 3. Writing SBML for MesoRD
- 4. Constructive Solid Geometry
- 5. The User Interface
- 6. Rates and state changes in MesoRD
- 7. Tutorial
- 8. Hacking
- Bibliography
- A. GNU Free Documentation License

**List of Figures**

- 1.1. Example of a three compartment geometry.
- 3.1.
The SBML definition
of
`UnitDefinition`

- 3.2.
The SBML definition
of
`Unit`

- 3.3.
The SBML definition of
`Compartment`

- 3.4.
The SBML definition of
`Species`

- 3.5.
The XML definition of
`SpeciesDiffusion`

- 3.6.
The XML definition of
`Diffusion`

- 3.7.
The SBML definition of
`Species`

- 3.8.
The SBML definition of
`Reaction`

- 3.9.
The SBML definition of
`SpeciesReference`

. - 3.10.
The SBML definition
of
`ModifierSpeciesReference`

- 3.11.
The SBML definition
of
`KineticLaw`

- 3.12.
The XML definition of
`MicroscopicParameters`

. - 3.13.
The XML definition of
`AssociationRateConst`

. - 3.14.
The XML definition of
`ReactionRadius`

. - 3.15.
The XML definition of
`DegreeOfDiffusionControl`

. - 4.1. A Simple Two-Dimensional Object
- 4.2. Constructive Solid Geometry Set Operations in Two Dimensions
- 4.3. The Utah Teapot in MesoRD CSG
- 4.4. A CSG Tree with Transformations
- 5.1. The GUI on Windows XP™
- 5.2. The available deterministic methods
- 5.3. The OpenGL Visualiser
- 7.1. Snapshot of simulation at 1 second simulation time.
- 7.2. Snapshot of simulation at 80 seconds simulation time.

**List of Tables**

**List of Examples**

- 3.1. The basic structure of an SBML file used in MesoRD is
- 3.2. Unit Definition.
- 3.3. Compartment Definition.
- 3.4. Species Definition.
- 3.5. Reaction Definition.
- 3.6. Reaction Definitions with scale dependent reaction rates.
- 4.1. Box Geometry
- 4.2. Cone Geometry
- 4.3. Cylinder Geometry
- 4.4. Mesh Geometry
- 4.5. Sphere Geometry
- 4.6. The
`compartment`

Primitive - 4.7. The
`rectangle`

Primitive - 4.8. The
`circle`

Primitive - 4.9. Difference Operation
- 4.10. Intersection Operation
- 4.11. Union Operation
- 4.12. Rotation Transformation
- 4.13. Scale Transformation
- 4.14. Shear Transformation
- 4.15. Translation Transformation
- 4.16. Box Periodic Boundary Condition
- 4.17. Cylinder Periodic Boundary Condition, or toroidal boundary condition