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2016 ; 144
(12
): 125104
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Asynchronous ?-leaping
#MMPMID27036481
J?drzejewski-Szmek Z
; Blackwell KT
J Chem Phys
2016[Mar]; 144
(12
): 125104
PMID27036481
show ga
Stochastic simulation of cell signaling pathways and genetic regulatory networks
has contributed to the understanding of cell function; however, investigation of
larger, more complicated systems requires computationally efficient algorithms.
?-leaping methods, which improve efficiency when some molecules have high copy
numbers, either use a fixed leap size, which does not adapt to changing state, or
recalculate leap size at a heavy computational cost. We present a hybrid
simulation method for reaction-diffusion systems which combines exact stochastic
simulation and ?-leaping in a dynamic way. Putative times of events are stored in
a priority queue, which reduces the cost of each step of the simulation. For
every reaction and diffusion channel at each step of the simulation the more
efficient of an exact stochastic event or a ?-leap is chosen. This new approach
removes the inherent trade-off between speed and accuracy in stiff systems which
was present in all ?-leaping methods by allowing each reaction channel to proceed
at its own pace. Both directions of reversible reactions and diffusion are
combined in a single event, allowing bigger leaps to be taken. This improves
efficiency for systems near equilibrium where forward and backward events are
approximately equally frequent. Comparison with existing algorithms and behaviour
for five test cases of varying complexity shows that the new method is almost as
accurate as exact stochastic simulation, scales well for large systems, and for
various problems can be significantly faster than ?-leaping.
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