Results 11 to 20 of about 669,188 (305)
Roles of network topology in the relaxation dynamics of simple chemical reaction network models [PDF]
Scientific ReportsUnderstanding the relationship between the structure of chemical reaction networks and their reaction dynamics is essential for unveiling the design principles of living organisms.
Yusuke Himeoka +3 more
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On Quantitative Comparison of Chemical Reaction Network Models [PDF]
Electronic Proceedings in Theoretical Computer Science, 2019 Chemical reaction networks (CRNs) provide a convenient language for modelling a broad variety of biological systems. These models are commonly studied with respect to the time series they generate in deterministic or stochastic simulations. Their dynamic
Ozan Kahramanoğulları
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Scaling limits of spatial compartment models for chemical reaction networks [PDF]
The Annals of Applied Probability, 2013 We study the effects of fast spatial movement of molecules on the dynamics of chemical species in a spatially heterogeneous chemical reaction network using a compartment model. The reaction networks we consider are either single- or multi-scale.
P. Pfaffelhuber, L. Popovic
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A chemical reaction network model of PURE
bioRxiv, 2023 Cell-free expression systems provide a method for rapid DNA circuit prototyping and functional protein synthesis. While crude extracts remain a black box with many components carrying out unknown reactions, the PURE system contains only the required ...
Zoila Jurado +2 more
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Uncoupled analysis of stochastic reaction networks in fluctuating environments. [PDF]
PLoS Computational Biology, 2014 The dynamics of stochastic reaction networks within cells are inevitably modulated by factors considered extrinsic to the network such as, for instance, the fluctuations in ribosome copy numbers for a gene regulatory network. While several recent studies
Christoph Zechner, Heinz Koeppl
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Journal of Cheminformatics, 2023 In recent years, it has been seen that artificial intelligence (AI) starts to bring revolutionary changes to chemical synthesis. However, the lack of suitable ways of representing chemical reactions and the scarceness of reaction data has limited the ...
Baiqing Li +8 more
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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
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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
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Uncertainty quantification for quantum chemical models of complex reaction networks.
Faraday Discussions, 2016 For the quantitative understanding of complex chemical reaction mechanisms, it is, in general, necessary to accurately determine the corresponding free energy surface and to solve the resulting continuous-time reaction rate equations for a continuous ...
J. Proppe +3 more
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Physics-informed machine learning for automatic model reduction in chemical reaction networks
Scientific ReportsPhysics-informed machine learning bridges the gap between the high fidelity of mechanistic models and the adaptive insights of artificial intelligence. In chemical reaction network modeling, this synergy proves valuable, addressing the high computational
Joseph Pateras +4 more
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