Results 11 to 20 of about 447,849 (263)

Comparison Theorems for Stochastic Chemical Reaction Networks. [PDF]

Bull Math Biol, 2023
AbstractContinuous-time Markov chains are frequently used as stochastic models for chemical reaction networks, especially in the growing field of systems biology. A fundamental problem for these Stochastic Chemical Reaction Networks (SCRNs) is to understand the dependence of the stochastic behavior of these systems on the chemical reaction rate ...
Campos FA, Bruno S, Fu Y, Del Vecchio D, Williams RJ.   +4 more
europepmc   +6 more sources

Exploring the programmability of autocatalytic chemical reaction networks [PDF]

Nature Communications
Networks of chemical reactions exhibit emergent properties under out-of-equilibrium conditions. Recent advances in systems chemistry demonstrate that networks with sufficient chemical complexity can be harnessed to emulate properties important for ...
Dmitrii V. Kriukov, Jurriaan Huskens, Albert S. Y. Wong   +2 more
doaj   +2 more sources

A Drive towards Thermodynamic Efficiency for Dissipative Structures in Chemical Reaction Networks [PDF]

Entropy, 2021
Dissipative accounts of structure formation show that the self-organisation of complex structures is thermodynamically favoured, whenever these structures dissipate free energy that could not be accessed otherwise.
Kai Ueltzhöffer, Lancelot Da Costa, Daniela Cialfi, Karl Friston   +3 more
doaj   +2 more sources

Gears in chemical reaction networks for optimizing energy transduction efficiency [PDF]

Nature Communications
Similarly to gear systems in vehicles, most chemical reaction networks (CRNs) involved in energy transduction have at their disposal multiple transduction pathways, each characterized by distinct efficiencies. We conceptualize these pathways as ‘chemical
Massimo Bilancioni, Massimiliano Esposito   +1 more
doaj   +2 more sources

Quantifying and comparing causal patterns in stochastic chemical reaction networks [PDF]

npj Systems Biology and Applications
Chemical reaction networks (CRNs) are broadly used to study biological systems via simulations. Gillespie’s Stochastic Simulation Algorithm (SSA) is commonly used to perform stochastic simulations with CRNs. Comparing two CRNs in such a setting relies on
Ozan Kahramanoğulları
doaj   +2 more sources

Grip on complexity in chemical reaction networks [PDF]

Beilstein Journal of Organic Chemistry, 2017
A new discipline of “systems chemistry” is emerging, which aims to capture the complexity observed in natural systems within a synthetic chemical framework.
Albert S. Y. Wong, Wilhelm T. S. Huck
doaj   +2 more sources

BioCRNpyler: Compiling chemical reaction networks from biomolecular parts in diverse contexts. [PDF]

PLoS Computational Biology, 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.
William Poole, Ayush Pandey, Andrey Shur, Zoltan A Tuza, Richard M Murray   +4 more
doaj   +2 more sources

Absolutely robust controllers for chemical reaction networks. [PDF]

J R Soc Interface, 2020
In this work, we design a type of controller that consists of adding a specific set of reactions to an existing mass-action chemical reaction network in order to control a target species. This set of reactions is effective for both deterministic and stochastic networks, in the latter case controlling the mean as well as the variance of the target ...
Kim J, Enciso G.
europepmc   +6 more sources

Syntactic Markovian Bisimulation for Chemical Reaction Networks [PDF]

, 2017
In chemical reaction networks (CRNs) with stochastic semantics based on continuous-time Markov chains (CTMCs), the typically large populations of species cause combinatorially large state spaces.
A Abate, A Vandin, C Autant, C Baier, D Gillespie, D Soloveichik, DT Gillespie, DT Huynh, F Ciocchetta, G Iacobelli, G Zavattaro, H Conzelmann, J Feret, J Heath, J Hillston, KG Larsen, L Cardelli, L Cardelli, L Cardelli, L Cardelli, L Cardelli, L Cardelli, M Kwiatkowska, M Tschaikowski, M Tschaikowski, M Tschaikowski, M Tschaikowski, MB Elowitz, ML Blinov, MW Sneddon, O Dushek, P Buchholz, R Paige, S Derisavi, S Gay, S Gilmore, TG Kurtz, V Danos, V Danos, Z Rózsa   +39 more
core   +4 more sources

Law of localization in chemical reaction networks

Physical Review Letters, 2016
In living cells, chemical reactions are connected by sharing their products and substrates, and form complex networks, e.g. metabolic pathways. Here we developed a theory to predict the sensitivity, i.e.
Mochizuki, Atsushi, Okada, Takashi
core   +4 more sources