Metabolism‐inspired chemical reaction networks for chemically driven dissipative oligoesterification [PDF]
Angew Chem Int Ed EnglYeonsoo Lim +9 more
openalex +2 more sources
Solving moment hierarchies for chemical reaction networks [PDF]
Journal of Physics A: Mathematical and Theoretical, 2017 The study of Chemical Reaction Networks (CRN's) is a very active field. Earlier well-known results \cite{Feinberg:def_01:87, Anderson:product_dist:10} identify a topological quantity called deficiency, for any CRN, which, when exactly equal to zero, leads to a unique factorized steady-state for these networks.
Supriya Krishnamurthy, Eric Smith
openaire +4 more sources
Programming Discrete Distributions with Chemical Reaction Networks [PDF]
Natural Computing, 2016 We explore the range of probabilistic behaviours that can be engineered with Chemical Reaction Networks (CRNs). We show that at steady state CRNs are able to "program" any distribution with finite support in $\mathbb{N}^m$, with $m \geq 1$. Moreover, any distribution with countable infinite support can be approximated with arbitrarily small error under
Cardelli, L, Kwiatkowska, M, Laurenti, L
openaire +8 more sources
Pathfinder─Navigating and Analyzing Chemical Reaction Networks with an Efficient Graph-Based Approach. [PDF]
J Chem Inf Model, 2023 While the field of first-principles explorations into chemical reaction space has been continuously growing, the development of strategies for analyzing resulting chemical reaction networks (CRNs) is lagging behind.
Türtscher PL, Reiher M.
europepmc +3 more sources
Programming and training rate-independent chemical reaction networks. [PDF]
Proc Natl Acad Sci U S A, 2022 Significance To program complex behavior in environments incompatible with electronic controllers such as within bioreactors or engineered cells, we turn to chemical information processors.
Vasić M +4 more
europepmc +3 more sources
Trade-offs between number fluctuations and response in nonequilibrium chemical reaction networks. [PDF]
Journal of Chemical Physics, 2023 We study the response of chemical reaction networks driven far from equilibrium to logarithmic perturbations of reaction rates. The response of the mean number of a chemical species is observed to be quantitively limited by number fluctuations and the ...
Hyun-Myung Chun, J. Horowitz
semanticscholar +1 more source
BioCRNpyler: Compiling chemical reaction networks from biomolecular parts in diverse contexts. [PDF]
PLoS Comput Biol, 2022 Biochemical interactions in systems and synthetic biology are often modeled with chemical reaction networks (CRNs). CRNs provide a principled modeling environment capable of expressing a huge range of biochemical processes.
Poole W +4 more
europepmc +2 more sources
Scaling methods for accelerating kinetic Monte Carlo simulations of chemical reaction networks [PDF]
J Chem Phys, 2019 Yen Ting Lin +2 more
openalex +2 more sources
Free-energy transduction in chemical reaction networks: From enzymes to metabolism. [PDF]
Journal of Chemical Physics, 2022 We provide a rigorous definition of free-energy transduction and its efficiency in arbitrary-linear or nonlinear-open chemical reaction networks (CRNs) operating at a steady state. Our method is based on the knowledge of the stoichiometric matrix and the
A. Wachtel, Riccardo Rao, M. Esposito
semanticscholar +1 more source
Thermodynamics of concentration vs flux control in chemical reaction networks. [PDF]
Journal of Chemical Physics, 2021 We investigate the thermodynamic implications of two control mechanisms of open chemical reaction networks. The first controls the concentrations of the species that are exchanged with the surroundings, while the other controls the exchange fluxes.
Francesco Avanzini, M. Esposito
semanticscholar +1 more source