Individual-Molecule Perspective Analysis of Chemical Reaction Networks: The Case of a Light-Driven Supramolecular Pump. [PDF]
Angew Chem Int Ed Engl, 2019 Sabatino A +4 more
europepmc +2 more sources
Forward and Backward Bisimulations for Chemical Reaction Networks [PDF]
, 2015 We present two quantitative behavioral equivalences over species of a chemical reaction network (CRN) with semantics based on ordinary differential equations.
Cardelli, Luca +3 more
core +4 more sources
Networking chemical robots for reaction multitasking [PDF]
Nature Communications, 2018 Abstract The development of the internet of things has led to an explosion in the number of networked devices capable of control and computing. However, whilst common place in remote sensing, these approaches have not impacted chemistry due to difficulty in developing systems flexible enough for experimental data collection. Herein we
Dario Caramelli +6 more
openaire +3 more sources
Uncertainty-aware prediction of chemical reaction yields with graph neural networks
Journal of Cheminformatics, 2022 In this paper, we present a data-driven method for the uncertainty-aware prediction of chemical reaction yields. The reactants and products in a chemical reaction are represented as a set of molecular graphs.
Youngchun Kwon +3 more
doaj +1 more source
Robust Stochastic Chemical Reaction Networks and Bounded Tau-Leaping [PDF]
, 2009 The behavior of some stochastic chemical reaction networks is largely unaffected by slight inaccuracies in reaction rates. We formalize the robustness of state probabilities to reaction rate deviations, and describe a formal connection between robustness
Soloveichik, David
core +2 more sources
Neutral theory of chemical reaction networks
, 2012 To what extent do the characteristic features of a chemical reaction network reflect its purpose and function? In general, one argues that correlations between specific features and specific functions are key to understanding a complex structure. However,
Baek S K +11 more
core +1 more source
Reaction networks as systems for resource allocation: a variational principle for their non-equilibrium steady states. [PDF]
PLoS ONE, 2012 Within a fully microscopic setting, we derive a variational principle for the non-equilibrium steady states of chemical reaction networks, valid for time-scales over which chemical potentials can be taken to be slowly varying: at stationarity the system ...
Andrea De Martino +3 more
doaj +1 more source
Concordant chemical reaction networks and the Species-Reaction Graph [PDF]
Mathematical Biosciences, 2013 In a recent paper it was shown that, for chemical reaction networks possessing a subtle structural property called concordance, dynamical behavior of a very circumscribed (and largely stable) kind is enforced, so long as the kinetics lies within the very broad and natural weakly monotonic class.
Shinar, Guy, Feinberg, Martin
openaire +3 more sources
A Language for Modeling and Optimizing Experimental Biological Protocols
Computation, 2021 Automation is becoming ubiquitous in all laboratory activities, moving towards precisely defined and codified laboratory protocols. However, the integration between laboratory protocols and mathematical models is still lacking.
Luca Cardelli +2 more
doaj +1 more source
Mechanism Deduction from Noisy Chemical Reaction Networks
, 2018 We introduce KiNetX, a fully automated meta-algorithm for the kinetic analysis of complex chemical reaction networks derived from semi-accurate but efficient electronic structure calculations. It is designed to (i) accelerate the automated exploration of
Proppe, Jonny, Reiher, Markus
core +1 more source