Solving the chemical master equation for monomolecular reaction systems analytically
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Publication:883795
DOI10.1007/s00285-006-0034-xzbMath1113.92032OpenAlexW2127535453WikidataQ51934002 ScholiaQ51934002MaRDI QIDQ883795
Wilhelm Huisinga, Tobias Jahnke
Publication date: 12 June 2007
Published in: Journal of Mathematical Biology (Search for Journal in Brave)
Full work available at URL: http://eprints.maynoothuniversity.ie/1729/1/JaHu2005MasterEquation.pdf
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Cites Work
- Unnamed Item
- Unnamed Item
- Unnamed Item
- A stochastic analysis of first-order reaction networks
- Multiscale stochastic simulation algorithm with stochastic partial equilibrium assumption for chemically reacting systems
- An introduction to probability theory with statistical applications
- An introduction to stochastic processes and their applications
- Computational cell biology
- Stochastic approaches for modelling in vivo reactions
- Numerical methods for strong solutions of stochastic differential equations: an overview
- On the solution of linear differential equations in Lie groups
- Adaptive simulation of hybrid stochastic and deterministic models for biochemical systems
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