Results 21 to 30 of about 136,245 (330)
A human-machine interface for automatic exploration of chemical reaction networks [PDF]
Nature CommunicationsAutonomous reaction network exploration algorithms offer a systematic approach to explore mechanisms of complex chemical processes. However, the resulting reaction networks are so vast that an exploration of all potentially accessible intermediates is ...
Miguel Steiner, Markus Reiher
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Gain and loss of function mutations in biological chemical reaction networks: a mathematical model with application to colorectal cancer cells. [PDF]
J Math Biol, 2021 Sommariva S, Caviglia G, Piana M.
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Self-selection of dissipative assemblies driven by primitive chemical reaction networks [PDF]
Nature Communications, 2018 Selection and persistence of chemical non-equilibrium species is crucial for the emergence of life and the exact mechanisms remain elusive. Here the authors show that phase separation is an efficient way to control selection of chemical species when ...
Marta Tena-Solsona +4 more
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Families of toric chemical reaction networks [PDF]
Journal of Mathematical Chemistry, 2023 We study families of chemical reaction networks whose positive steady states are toric, and therefore can be parameterized by monomials. Families are constructed algorithmically from a core network; we show that if a family member is multistationary ...
Helmer, Martin, Adamer, Michael
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Independent Decompositions of Chemical Reaction Networks [PDF]
Bulletin of Mathematical Biology, 2021 A chemical reaction network (CRN) is composed of reactions that can be seen as interactions among entities called species, which exist within the system. Endowed with kinetics, CRN has a corresponding set of ordinary differential equations (ODEs). In Chemical Reaction Network Theory, we are interested with connections between the structure of the CRN ...
Bryan S. Hernandez +1 more
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The Exploration of Chemical Reaction Networks [PDF]
Annual Review of Physical Chemistry, 2020 Modern computational chemistry has reached a stage at which massive exploration into chemical reaction space with unprecedented resolution with respect to the number of potentially relevant molecular structures has become possible. Various algorithmic advances have shown that such structural screenings must and can be automated and routinely carried ...
Unsleber, Jan P., Reiher, Markus
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Concordant chemical reaction networks [PDF]
Mathematical Biosciences, 2012 We describe a large class of chemical reaction networks, those endowed with a subtle structural property called concordance. We show that the class of concordant networks coincides precisely with the class of networks which, when taken with any weakly monotonic kinetics, invariably give rise to kinetic systems that are injective --- a quality that ...
Shinar, Guy, Feinberg, Martin
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On the multistationarity of chemical reaction networks [PDF]
Journal of Theoretical Biology, 2019 We present a new conjecture about a necessary condition that a (bio)chemical network has to satisfy for it to exhibit multistationarity. According to a Theorem of Feliu and Wiuf [27, 12], the conjecture is known for strictly monotonic kinetics. We give several examples illustrating our conjecture.
Kaufman, Marcelle, Christophe Soulé
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Siphons in Chemical Reaction Networks [PDF]
Bulletin of Mathematical Biology, 2010 Siphons in a chemical reaction system are subsets of the species that have the potential of being absent in a steady state. We present a characterization of minimal siphons in terms of primary decomposition of binomial ideals, we explore the underlying geometry, and we demonstrate the effective computation of siphons using computer algebra software ...
Shiu, Anne, Sturmfels, Bernd
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Reachability in Restricted Chemical Reaction Networks
Theoretical Computer Science, 2023 The popularity of molecular computation has given rise to several models of abstraction, one of the more recent ones being Chemical Reaction Networks (CRNs). These are equivalent to other popular computational models, such as Vector Addition Systems and Petri-Nets, and restricted versions are equivalent to Population Protocols. This paper continues the
Robert M. Alaniz +7 more
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