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BMCBI
2010
131views more  BMCBI 2010»
14 years 10 months ago
A comparison of approximation techniques for variance-based sensitivity analysis of biochemical reaction systems
Background: Sensitivity analysis is an indispensable tool for the analysis of complex systems. In a recent paper, we have introduced a thermodynamically consistent variance-based ...
Hong-Xuan Zhang, John Goutsias
BMCBI
2010
259views more  BMCBI 2010»
14 years 4 months 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...
SIAMSC
2008
131views more  SIAMSC 2008»
14 years 9 months ago
Fast Monte Carlo Simulation Methods for Biological Reaction-Diffusion Systems in Solution and on Surfaces
Many important physiological processes operate at time and space scales far beyond those accessible to atom-realistic simulations, and yet discrete stochastic rather than continuum...
Rex A. Kerr, Thomas M. Bartol, Boris Kaminsky, Mar...
ACAL
2009
Springer
15 years 4 months ago
Multivesicular Assemblies as Real-World Testbeds for Embryogenic Evolutionary Systems
Embryogenic evolution emulates in silico cell-like entities to get more powerful methods for complex evolutionary tasks. As simulations have to from the biological model, implicit ...
Maik Hadorn, Peter Eggenberger Hotz
POPL
2008
ACM
15 years 10 months ago
Systems biology, models, and concurrency
Models will play a central role in the representation, storage, manipulation, and communication of knowledge in systems biology. Models capable of fulfilling such a role will like...
Walter Fontana