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RELEVANT CYCLES IN CHEMICAL REACTION NETWORKS [PDF]
Advances in Complex Systems, 2001 We characterize the distributions of short cycles in a large metabolic network previously shown to have small world characteristics and a power law degree distribution. Compared with three classes of random networks, including Erdős–Rényi random graphs and synthetic small world networks of the same connectivity, both the metabolic network and models ...
PETRA M. GLEISS +3 more
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DNA‐Based Chemical Reaction Networks
ChemBioChem, 2019AbstractMotivated by complex molecular networks of biological organisms, which enable control of the temporal and spatial concentrations of molecules, the bottom‐up development of artificial chemical reaction networks has received renewed interest from biochemists.
Fan Li, Mingshu Xiao, Hao Pei
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Chemical reaction network sensitivity analysis
The Journal of Chemical Physics, 1984Traditional sensitivity analysis of a chemical reaction system’s periodic trajectory shows how the oscillation depends on the reaction rate constants. We develop sensitivity analysis within the framework of a stoichiometric network analysis, which is a theory that relates the dynamics of complex chemical reaction systems to feedback loops in the ...
R. Larter, B. L. Clarke
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Embracing Noise in Chemical Reaction Networks
Bulletin of Mathematical Biology, 2019We provide a short review of stochastic modeling in chemical reaction networks for mathematical and quantitative biologists. We use as case studies two publications appearing in this issue of the Bulletin, on the modeling of quasi-steady-state approximations and cell polarity.
Enciso, German, Kim, Jinsu
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Reconstructing chemical reaction networks
Proceedings of the 14th ACM SIGKDD international conference on Knowledge discovery and data mining, 2008We present an approach to reconstructing chemical reaction networks from time series measurements of the concentrations of the molecules involved. Our solution strategy combines techniques from numerical sensitivity analysis and probabilistic graphical models.
Yong Ju Cho +2 more
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Chemical Reaction Networks for Computing Polynomials
ACS Synthetic Biology, 2016Chemical reaction networks (CRNs) provide a fundamental model in the study of molecular systems. Widely used as formalism for the analysis of chemical and biochemical systems, CRNs have received renewed attention as a model for molecular computation.
Sayed Ahmad, Salehi +2 more
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Chemical reaction dynamics part II: Reaction networks
Archive for Rational Mechanics and Analysis, 1974The notion of a chemical reaction network is made precise in terms of electrical network theory by demonstrating that the mathematical formulation of chemical reactions can be viewed as a subset of abstract circuit theory. An algorithm is presented for constructing linear graph and bond graph representations of chemical reaction systems.
Alan S. Perelson, George F. Oster
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AUTOGRAPH: Chemical Reaction Networks in 3D
Journal of Chemical Information and ModelingUnderstanding and analyzing large-scale reaction networks is a fundamental challenge due to their complexity and size, often beyond human comprehension. In this paper, we introduce AUTOGRAPH, the first web-based tool designed for the interactive three-dimensional (3D) visualization and construction of reaction networks. AUTOGRAPH emphasizes ease of use,
Philipp Kuboth +3 more
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A tutorial on Chemical Reaction Networks dynamics
2009 European Control Conference (ECC), 2009zbMATH Open Web Interface contents unavailable due to conflicting licenses.
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