TY - JOUR

T1 - Stochastic analysis of dimerization systems

AU - Barzel, Baruch

AU - Biham, Ofer

PY - 2009/9/16

Y1 - 2009/9/16

N2 - The process of dimerization, in which two monomers bind to each other and form a dimer, is common in nature. This process can be modeled using rate equations, from which the average copy numbers of the reacting monomers and of the product dimers can then be obtained. However, the rate equations apply only when these copy numbers are large. In the limit of small copy numbers the system becomes dominated by fluctuations, which are not accounted for by the rate equations. In this limit one must use stochastic methods such as direct integration of the master equation or Monte Carlo simulations. These methods are computationally intensive and rarely succumb to analytical solutions. Here we use the recently introduced moment equations which provide a highly simplified stochastic treatment of the dimerization process. Using this approach, we obtain an analytical solution for the copy numbers and reaction rates both under steady-state conditions and in the time-dependent case. We analyze three different dimerization processes: dimerization without dissociation, dimerization with dissociation, and heterodimer formation. To validate the results we compare them with the results obtained from the master equation in the stochastic limit and with those obtained from the rate equations in the deterministic limit. Potential applications of the results in different physical contexts are discussed.

AB - The process of dimerization, in which two monomers bind to each other and form a dimer, is common in nature. This process can be modeled using rate equations, from which the average copy numbers of the reacting monomers and of the product dimers can then be obtained. However, the rate equations apply only when these copy numbers are large. In the limit of small copy numbers the system becomes dominated by fluctuations, which are not accounted for by the rate equations. In this limit one must use stochastic methods such as direct integration of the master equation or Monte Carlo simulations. These methods are computationally intensive and rarely succumb to analytical solutions. Here we use the recently introduced moment equations which provide a highly simplified stochastic treatment of the dimerization process. Using this approach, we obtain an analytical solution for the copy numbers and reaction rates both under steady-state conditions and in the time-dependent case. We analyze three different dimerization processes: dimerization without dissociation, dimerization with dissociation, and heterodimer formation. To validate the results we compare them with the results obtained from the master equation in the stochastic limit and with those obtained from the rate equations in the deterministic limit. Potential applications of the results in different physical contexts are discussed.

UR - http://www.scopus.com/inward/record.url?scp=70349971164&partnerID=8YFLogxK

U2 - 10.1103/PhysRevE.80.031117

DO - 10.1103/PhysRevE.80.031117

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AN - SCOPUS:70349971164

SN - 1539-3755

VL - 80

JO - Physical Review E

JF - Physical Review E

IS - 3

M1 - 031117

ER -