Estimation and discrimination of stochastic biochemical circuits from time-lapse microscopy data. [PDF]
PLoS ONE, 2012 The ability of systems and synthetic biologists to observe the dynamics of cellular behavior is hampered by the limitations of the sensors, such as fluorescent proteins, available for use in time-lapse microscopy.
David Thorsley, Eric Klavins
doaj +1 more source
Piecewise linear models of chemical reaction networks
, 2012 We show that certain non-linear dynamical systems with non-linearities in the form of Hill functions, can be approximated by piecewise linear dynamical systems. The resulting piecewise systems have closed form solutions that can be used to understand the behavior of the fully nonlinear system.
Kumar, Ajit, Josić, Krešimir
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Exploiting network topology for large-scale inference of nonlinear reaction models
, 2019 The development of chemical reaction models aids understanding and prediction in areas ranging from biology to electrochemistry and combustion. A systematic approach to building reaction network models uses observational data not only to estimate unknown
Galagali, Nikhil, Marzouk, Youssef M.
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Analytical Formulas of Molecular Ion Abundances and N2H+ Ring in Protoplanetary Disks [PDF]
, 2015 We investigate the chemistry of ion molecules in protoplanetary disks, motivated by the detection of N$_2$H$^+$ ring around TW Hya. While the ring inner radius coincides with the CO snow line, it is not apparent why N$_2$H$^+$ is abundant outside the CO ...
Aikawa, Yuri +3 more
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Missing links as a source of seemingly variable constants in complex reaction networks
Physical Review Research, 2020 A major challenge in network science is to determine parameters governing complex network dynamics from experimental observations and theoretical models.
Zachary G. Nicolaou, Adilson E. Motter
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Efficient multi-fidelity computation of blood coagulation under flow.
PLoS Computational Biology, 2023 Clot formation is a crucial process that prevents bleeding, but can lead to severe disorders when imbalanced. This process is regulated by the coagulation cascade, a biochemical network that controls the enzyme thrombin, which converts soluble fibrinogen
Manuel Guerrero-Hurtado +8 more
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Asymptotic analysis of multiscale approximations to reaction networks
, 2006 A reaction network is a chemical system involving multiple reactions and chemical species. Stochastic models of such networks treat the system as a continuous time Markov chain on the number of molecules of each species with reactions as possible ...
Ball, Karen +3 more
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Chemical master versus chemical langevin for first-order reaction networks [PDF]
, 2008 Markov jump processes are widely used to model interacting species in circumstances where discreteness and stochasticity are relevant. Such models have been particularly successful in computational cell biology, and in this case, the interactions are ...
Higham, Desmond J., Khanin, Raya
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Uncertainty quantification for quantum chemical models of complex reaction networks
Faraday Discussions, 2016 For the quantitative understanding of complex chemical reaction mechanisms, it is, in general, necessary to accurately determine the corresponding free energy surface and to solve the resulting continuous-time reaction rate equations for a continuous state space.
Proppe, Jonny +3 more
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A scalable algorithm to explore the Gibbs energy landscape of genome-scale metabolic networks. [PDF]
PLoS Computational Biology, 2012 The integration of various types of genomic data into predictive models of biological networks is one of the main challenges currently faced by computational biology.
Daniele De Martino +3 more
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