Biology – Quantitative Biology – Quantitative Methods
Scientific paper
2010-10-02
Physical Review E, 83, 056701, 2011
Biology
Quantitative Biology
Quantitative Methods
8 pages, 3 figures
Scientific paper
10.1103/PhysRevE.83.056701
We present an efficient and exact Monte Carlo algorithm to simulate reversible aggregation of particles with dedicated binding sites. This method introduces a novel data structure of dynamic bond tree to record clusters and sequences of bond formations. The algorithm achieves a constant time cost for processing cluster association and a cost between $\mathcal{O}(\log M)$ and $\mathcal{O}(M)$ for processing bond dissociation in clusters with $M$ bonds. The algorithm is statistically exact and can reproduce results obtained by the standard method. We applied the method to simulate a trivalent ligand and a bivalent receptor clustering system and obtained an average scaling of $\mathcal{O}(M^{0.45})$ for processing bond dissociation in acyclic aggregation, compared to a linear scaling with the cluster size in standard methods. The algorithm also demands substantially less memory than the conventional method.
Chang Qiang
Yang Jin
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