Spatial Simulations in Systems Biology: From Molecules to Cells
Open Access
- 20 June 2012
- journal article
- review article
- Published by MDPI AG in International Journal of Molecular Sciences
- Vol. 13 (6), 7798-7827
- https://doi.org/10.3390/ijms13067798
Abstract
Cells are highly organized objects containing millions of molecules. Each biomolecule has a specific shape in order to interact with others in the complex machinery. Spatial dynamics emerge in this system on length and time scales which can not yet be modeled with full atomic detail. This review gives an overview of methods which can be used to simulate the complete cell at least with molecular detail, especially Brownian dynamics simulations. Such simulations require correct implementation of the diffusion-controlled reaction scheme occurring on this level. Implementations and applications of spatial simulations are presented, and finally it is discussed how the atomic level can be included for instance in multi-scale simulation methods.Keywords
This publication has 179 references indexed in Scilit:
- Membrane Clustering and the Role of Rebinding in Biochemical SignalingBiophysical Journal, 2012
- Local Motion Analysis Reveals Impact of the Dynamic Cytoskeleton on Intracellular SubdiffusionBiophysical Journal, 2012
- Channeling by Proximity: The Catalytic Advantages of Active Site Colocalization Using Brownian DynamicsThe Journal of Physical Chemistry Letters, 2010
- Cellular Dynamic Simulator: An Event Driven Molecular Simulation Environment for Cellular PhysiologyNeuroinformatics, 2010
- A new multicompartmental reaction-diffusion modeling method links transient membrane attachment of E. coli MinE to E-ring formationSystems and Synthetic Biology, 2009
- Stochastic Simulation of Signal Transduction: Impact of the Cellular Architecture on DiffusionBiophysical Journal, 2009
- Protein Structure Prediction by Pro-Sp3-TASSERBiophysical Journal, 2009
- Deterministic Limit of Stochastic Chemical KineticsThe Journal of Physical Chemistry B, 2009
- Input–output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic dataMolecular Systems Biology, 2009
- Rule-Based Modelling of Cellular SignallingPublished by Springer Science and Business Media LLC ,2007