# Particle-Based Stochastic Simulation in Systems Biology

@article{Tolle2006ParticleBasedSS, title={Particle-Based Stochastic Simulation in Systems Biology}, author={Dominic P. Tolle and Nicolas Le Nov{\`e}re}, journal={Current Bioinformatics}, year={2006}, volume={1}, pages={315-320} }

Computational modeling and simulation have become invaluable tools for the biological sciences. Both aid in the formulation of new hypothesis and supplement traditional experimental research. Many different types of models us- ing various mathematical formalisms can be created to represent any given biological system. Here we review a class of modeling techniques based on particle-based stochastic approaches. In these models, every reacting molecule is repre- sented individually. Reactions…

## 44 Citations

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## References

SHOWING 1-10 OF 56 REFERENCES

### Space as the final frontier in stochastic simulations of biological systems

- BiologyFEBS letters
- 2005

### Microbial cell modeling via reacting diffusive particles

- Biology
- 2005

A particle-based simulator called ChemCell is described that is developing with the goal of modeling the protein chemistry of biological cells for phenomena where spatial effects are important and interesting computational issues that arise in particle- based cell modeling are highlighted.

### Green's-function reaction dynamics: a particle-based approach for simulating biochemical networks in time and space.

- PhysicsThe Journal of chemical physics
- 2005

The main idea of GFRD is to exploit the exact solution of the Smoluchoswki equation to set up an event-driven algorithm, which combines in one step the propagation of the particles in space with the reactions between them.

### Green's-function reaction dynamics: a particle-based approach for simulating biochemical networks in time and space.

- Physics
- 2005

We have developed a new numerical technique, called Green's-function reaction dynamics (GFRD), that makes it possible to simulate biochemical networks at the particle level and in both time and…

### Stochastic simulation of chemical reactions with spatial resolution and single molecule detail

- Chemistry, PhysicsPhysical biology
- 2004

Methods are presented for simulating chemical reaction networks with a spatial resolution that is accurate to nearly the size scale of individual molecules. Using an intuitive picture of chemical…

### Automatic generation of cellular reaction networks with Moleculizer 1.0

- Computer ScienceNature Biotechnology
- 2005

This work describes an approach to the exact stochastic simulation of biochemical networks that emphasizes the contribution of protein complexes to these systems and generates much smaller reaction networks, which can be exported to other simulators for further analysis.

### Exact Stochastic Simulation of Coupled Chemical Reactions

- Physics
- 1977

There are two formalisms for mathematically describing the time behavior of a spatially homogeneous chemical system: The deterministic approach regards the time evolution as a continuous, wholly…

### STOCHSIM: modelling of stochastic biomolecular processes

- Computer ScienceBioinform.
- 2001

SUMMARY
STOCHSIM is a stochastic simulator for chemical reactions. Molecules are represented as individual software objects that react according to probabilities derived from concentrations and rate…

### Space in systems biology of signaling pathways – towards intracellular molecular crowding in silico

- BiologyFEBS letters
- 2005

### SmartCell, a framework to simulate cellular processes that combines stochastic approximation with diffusion and localisation: analysis of simple networks.

- EngineeringSystems biology
- 2004

The results show that this factor might play an important role in the response of networks and cannot be neglected in cell simulations, and the impact of localisation on the behaviour of simple well-defined networks, previously analysed with differential equations.