Results 1 to 10 of about 503,473 (274)

Roles of network topology in the relaxation dynamics of simple chemical reaction network models [PDF]

Scientific Reports
Understanding 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, Julius B. Kirkegaard, Namiko Mitarai, Sandeep Krishna   +3 more
doaj   +6 more sources

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
doaj   +5 more sources

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
doaj   +7 more sources

Scaling limits of spatial compartment models for chemical reaction networks

The Annals of Applied Probability, 2015
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.
Pfaffelhuber, Peter, Popovic, Lea
openaire   +6 more sources

Physics-informed machine learning for automatic model reduction in chemical reaction networks

Scientific Reports
Physics-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, Colin Zhang, Shriya Majumdar, Ayush Pal, Preetam Ghosh   +4 more
doaj   +3 more sources

Linear stability analysis of chemical mechanism, Listanalchem: A tool for the search of spontaneous mirror symmetry breaking

MethodsX, 2023
Homochirality, the phenomenon by which one of two virtually identical (non-superimposable mirror images) compounds is favored over the other in the chemistry of life, has been regarded as a requisite for the emergence of all living things on earth ...
Elkin Cruz, Andrés Montoya, Jesús Ágreda   +2 more
doaj   +1 more source

The GRETOBAPE Gas-phase Reaction Network: The Importance of Being Exothermic

The Astrophysical Journal Supplement Series, 2023
The gas-phase reaction networks are the backbone of astrochemical models. However, due to their complexity and nonlinear impact on the astrochemical modeling, they can be the first source of error in the simulations if incorrect reactions are present ...
Lorenzo Tinacci, Simón Ferrada-Chamorro, Cecilia Ceccarelli, Stefano Pantaleone, Daniela Ascenzi, Andrea Maranzana, Nadia Balucani, Piero Ugliengo   +7 more
doaj   +1 more source

Piecewise Linear and Boolean Models of Chemical Reaction Networks [PDF]

Bulletin of Mathematical Biology, 2014
This is an extension of previous work arXiv:1201 ...
Veliz-Cuba, Alan, Kumar, Ajit, Josić, Krešimir   +2 more
openaire   +4 more sources

Reaction Networks for Interstellar Chemical Modelling: Improvements and Challenges [PDF]

Space Science Reviews, 2010
Accepted for publication in Space Science ...
Wakelam, Valentine, Smith, I. W. M., Herbst, E., Troe, J., Geppert, W., Linnartz, H., Oberg, K., Roueff, E., Agúndez, M., Pernot, P., Cuppen, H. M., Loison, J. -C., Talbi, D.   +12 more
openaire   +4 more sources

A deep learning framework for accurate reaction prediction and its application on high-throughput experimentation data

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, Shimin Su, Chan Zhu, Jie Lin, Xinyue Hu, Lebin Su, Zhunzhun Yu, Kuangbiao Liao, Hongming Chen   +8 more
doaj   +1 more source