Results 21 to 30 of about 617,908 (340)
Piecewise linear models of chemical reaction networks
, 2012 We show that certain non-linear dynamical systems with non-linearities in the form of Hill functions, can be approximated by piecewise linear dynamical systems. The resulting piecewise systems have closed form solutions that can be used to understand the behavior of the fully nonlinear system.
Aditya Kumar, Krešimir Josić́
openalex +4 more sources
Evolutionary origin of power-laws in a biochemical reaction network: embedding the distribution of abundance into topology. [PDF]
Physical review. E, Statistical, nonlinear, and soft matter physics, 2005 The evolutionary origin of general statistics in a biochemical reaction network is studied here to explain the power-law distribution of reaction links and the power-law distribution of chemical abundance.
C. Furusawa, K. Kaneko
semanticscholar +3 more sources
An algebraic characterization of self-generating chemical reaction networks using semigroup models [PDF]
Journal of Mathematical Biology, 2023 AbstractThe ability of a chemical reaction network to generate itself by catalyzed reactions from constantly present environmental food sources is considered a fundamental property in origin-of-life research. Based on Kaufmann’s autocatalytic sets, Hordijk and Steel have constructed the versatile formalism of catalytic reaction systems (CRS) to model ...
Dimitri Loutchko
openalex +4 more sources
Mathematical Methods for Modeling Chemical Reaction Networks [PDF]
, 2016 AbstractCancer’s cellular behavior is driven by alterations in the processes that cells use to sense and respond to diverse stimuli. Underlying these processes are a series of chemical processes (enzyme-substrate, protein-protein, etc.). Here we introduce a set of mathematical techniques for describing and characterizing these processes.
J.F. Carden +4 more
openalex +2 more sources
Comprehensive review of models and methods for inferences in bio-chemical reaction networks [PDF]
Frontiers in Genetics, 2019 Key processes in biological and chemical systems are described by networks of chemical reactions. From molecular biology to biotechnology applications, computational models of reaction networks are used extensively to elucidate their non-linear dynamics.
Pavel Loskot +2 more
openalex +10 more sources
Forward and Backward Bisimulations for Chemical Reaction Networks [PDF]
International Conference on Concurrency Theory, 2015 We present two quantitative behavioral equivalences over species of a chemical reaction network (CRN) with semantics based on ordinary differential equations.
L. Cardelli +3 more
semanticscholar +6 more sources
Evolution of Autocatalytic Sets in Computational Models of Chemical Reaction Networks [PDF]
Origins of Life and Evolution of Biospheres, 2015 Several computational models of chemical reaction networks have been presented in the literature in the past, showing the appearance and (potential) evolution of autocatalytic sets. However, the notion of autocatalytic sets has been defined differently in different modeling contexts, each one having some shortcoming or limitation.
Wim Hordijk
openalex +4 more sources
Nonequilibrium fluctuations of chemical reaction networks at criticality: The Schlögl model as paradigmatic case [PDF]
The Journal of Chemical PhysicsChemical reaction networks can undergo nonequilibrium phase transitions upon variation in external control parameters, such as the chemical potential of a species. We investigate the flux in the associated chemostats that is proportional to the entropy production and its critical fluctuations within the Schlögl model.
Benedikt Remlein, Udo Seifert
+7 more sources
Modeling chemical reaction networks on the Pontryagin bundle with the Hamilton-Pontryagin approach
IFAC-PapersOnLine, 2015 Abstract The Lagrange-d'Alembert-Pontryagin principle is a versatile approach to model dynamical systems including resistive forces from the Lagrangian view. We show in this work, how this method can be applied to open stoichiometric reaction networks.
Henning Lindhorst, Steffen Waldherr
openalex +3 more sources
Continuous Time Markov Chain Models for Chemical Reaction Networks [PDF]
, 2011 A reaction network is a chemical system involving multiple reactions and chemical species. The simplest stochastic models of such networks treat the system as a continuous time Markov chain with the state being the number of molecules of each species and with reactions modeled as possible transitions of the chain.
David F. Anderson, Thomas G. Kurtz
openaire +3 more sources