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CATEGORIES:Isaac Newton Institute Seminar Series
SUMMARY:Hybrid modelling of stochastic chemical kinetics -
Andrew Duncan (University of Sussex\; The Alan Tu
ring Institute)
DTSTART;TZID=Europe/London:20160407T094500
DTEND;TZID=Europe/London:20160407T103000
UID:TALK65367AThttp://talks.cam.ac.uk
URL:http://talks.cam.ac.uk/talk/index/65367
DESCRIPTION: Co-authors: Radek Erban (University o
f Oxford)\, Kostantinos Zygalakis (University of
Edinburgh)
It is well k
nown that stochasticity can play a fundamental rol
e in various biochemical processes\, such as cell
regulatory networks and enzyme cascades. Isother
mal\, well-mixed systems can be adequately modelle
d by Markov processes and\, for such systems\, me
thods such as Gillespie'\;s algorithm are typic
ally employed. While such schemes are easy to imp
lement and are exact\, the computational cost of
simulating such systems can become prohibitive as
the frequency of the reaction events increases. T
his has motivated numerous coarse grained schemes
\, where the "fast" reactions are approximated eit
her using Langevin dynamics or deterministically.
While such approaches provide a good approximati
on for systems where all reactants are present in
large concentrations\, the approximation breaks d
own when the fast chemical species exist in small
concentrations\, giving rise to significant error
s in the simulation. This is particularly problem
atic when using such methods to compute statistic
s of extinction times for chemical species\, as we
ll as computing observables of cell cycle models.
In this talk\, we present a hybrid scheme for si
mulating well-mixed stochastic kinetics\, using Gi
llepsie-type dynamics to simulate the network in
regions of low reactant concentration\, and chemic
al Langevin dynamics when the concentrations of a
ll species is large. These two regimes are couple
d via an intermediate region in which a "blended"&
#39\; jump-diffusion model is introduced. Example
s of gene regulatory networks involving reactions
occurring at multiple scales\, as well as a cell-
cycle model are simulated\, using the exact and h
ybrid scheme\, and compared\, both in terms weak
error\, as well as computational cost.
LOCATION:Seminar Room 1\, Newton Institute
CONTACT:INI IT
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