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» Stochastic Model of Protease-Ligand Reactions
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CORR
2010
Springer
174views Education» more  CORR 2010»
13 years 5 months ago
Hybrid Numerical Solution of the Chemical Master Equation
We present a numerical approximation technique for the analysis of continuous-time Markov chains that describe networks of biochemical reactions and play an important role in the ...
Thomas A. Henzinger, Maria Mateescu, Linar Mikeev,...
BMCBI
2010
259views more  BMCBI 2010»
13 years 16 days ago
Rule-based spatial modeling with diffusing, geometrically constrained molecules
Background: We suggest a new type of modeling approach for the coarse grained, particle-based spatial simulation of combinatorially complex chemical reaction systems. In our appro...
Gerd Gruenert, Bashar Ibrahim, Thorsten Lenser, Ma...
IPPS
2006
IEEE
13 years 11 months ago
Performance analysis of stochastic process algebra models using stochastic simulation
We present a translation of a generic stochastic process algebra model into a form suitable for stochastic simulation. By systematically generating rate equations from a process d...
Jeremy T. Bradley, Stephen T. Gilmore, Nigel Thoma...
BMCBI
2004
323views more  BMCBI 2004»
13 years 5 months ago
Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks
Background: Intrinsic fluctuations due to the stochastic nature of biochemical reactions can have large effects on the response of biochemical networks. This is particularly true ...
David Adalsteinsson, David McMillen, Timothy C. El...
ICLP
2009
Springer
14 years 6 months ago
Constraint Based Languages for Biological Reactions
In this paper, we study the modelization of biochemical reaction by using concurrent constraint programming idioms. In particular we will consider the stochastic concurrent constra...
Marco Bottalico, Stefano Bistarelli