Coarse-grained molecular simulation of diffusion and reaction kinetics in a crowded virtual cytoplasm.

@article{Ridgway2008CoarsegrainedMS,
  title={Coarse-grained molecular simulation of diffusion and reaction kinetics in a crowded virtual cytoplasm.},
  author={Douglas Ridgway and Gordon Broderick and Ana Lopez-Campistrous and Melania Ru'aini and Philip M. Winter and Matthew J. Hamilton and Pierre A. Boulanger and Andriy Kovalenko and Michael J. Ellison},
  journal={Biophysical journal},
  year={2008},
  volume={94 10},
  pages={3748-59}
}
We present a general-purpose model for biomolecular simulations at the molecular level that incorporates stochasticity, spatial dependence, and volume exclusion, using diffusing and reacting particles with physical dimensions. To validate the model, we first established the formal relationship between the microscopic model parameters (timestep, move length, and reaction probabilities) and the macroscopic coefficients for diffusion and reaction rate. We then compared simulation results with… CONTINUE READING

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