scholarly journals Parameter Estimation of Kinetic Rates in Stochastic Reaction Networks by the EM Method

2008 ◽  
Author(s):  
Andr Horv ◽  
Daniele Manini
Keyword(s):  
Parameter Estimation ◽  
Reaction Networks ◽  
Kinetic Rates ◽  
Em Method ◽  
Stochastic Reaction ◽  
Stochastic Reaction Networks

scholarly journals Fast reactions with non-interacting species in stochastic reaction networks

2022 ◽  
Vol 19 (3) ◽  
pp. 2720-2749
Author(s):  
Linard Hoessly ◽  
◽  
Carsten Wiuf
Keyword(s):  
Markov Process ◽  
Sufficient Conditions ◽  
Reaction Network ◽  
Reaction Networks ◽  
Unknown Parameters ◽  
Interacting Species ◽  
Fast Reactions ◽  
Kinetic Rates ◽  
Stochastic Reaction ◽  
Stochastic Reaction Networks

<abstract><p>We consider stochastic reaction networks modeled by continuous-time Markov chains. Such reaction networks often contain many reactions, potentially occurring at different time scales, and have unknown parameters (kinetic rates, total amounts). This makes their analysis complex. We examine stochastic reaction networks with non-interacting species that often appear in examples of interest (e.g. in the two-substrate Michaelis Menten mechanism). Non-interacting species typically appear as intermediate (or transient) chemical complexes that are depleted at a fast rate. We embed the Markov process of the reaction network into a one-parameter family under a two time-scale approach, such that molecules of non-interacting species are degraded fast. We derive simplified reaction networks where the non-interacting species are eliminated and that approximate the scaled Markov process in the limit as the parameter becomes small. Then, we derive sufficient conditions for such reductions based on the reaction network structure for both homogeneous and time-varying stochastic settings, and study examples and properties of the reduction.</p></abstract>

scholarly journals Accelerated Sensitivity Analysis in High-Dimensional Stochastic Reaction Networks

PLoS ONE ◽  
2015 ◽  
Vol 10 (7) ◽  
pp. e0130825 ◽  
Author(s):  
Georgios Arampatzis ◽  
Markos A. Katsoulakis ◽  
Yannis Pantazis
Keyword(s):  
Sensitivity Analysis ◽  
Reaction Networks ◽  
High Dimensional ◽  
Stochastic Reaction ◽  
Stochastic Reaction Networks

scholarly journals Adaptive hybrid simulations for multiscale stochastic reaction networks

2015 ◽  
Vol 142 (3) ◽  
pp. 034118 ◽  
Author(s):  
Benjamin Hepp ◽  
Ankit Gupta ◽  
Mustafa Khammash
Keyword(s):  
Reaction Networks ◽  
Stochastic Reaction ◽  
Stochastic Reaction Networks ◽  
Hybrid Simulations
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