Comprehensive Review of Models and Methods for Inferences in Bio-Chemical Reaction Networks [PDF]
Frontiers in Genetics, 2019 Key processes in biological and chemical systems are described by networks of chemical reactions. From molecular biology to biotechnology applications, computational models of reaction networks are used extensively to elucidate their non-linear dynamics.
Loskot, P., Atitey, K., Mihaylova, L.
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Automatic reaction to a chemical event detected by a low-cost wireless chemical sensing network [PDF]
, 2009 A test-scale wireless chemical sensor network (WCSN) has been deployed within a controlled Environmental Chamber (EC). The combined signals from the WCSN were used to initiate a controllable response to the detected chemical event.
Corcoran, Brian +7 more
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A Theoretical Approach to the Complex Chemical Evolution of Phosphorus in the Interstellar Medium
The Astrophysical Journal, 2023 The study of phosphorus chemistry in the interstellar medium has become a topic of growing interest in astrobiology because it is plausible that a wide range of P-bearing molecules were introduced in the early Earth by the impact of asteroids and comets ...
Marina Fernández-Ruz +2 more
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Indistinguishability and identifiability of kinetic models for the MurC reaction in peptidoglycan biosynthesis [PDF]
, 2009 An important question in Systems Biology is the design of experiments that enable discrimination between two (or more) competing chemical pathway models or biological mechanisms.
Roper, D. +23 more
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Prediction of Compound Synthesis Accessibility Based on Reaction Knowledge Graph
Molecules, 2022 With the increasing application of deep-learning-based generative models for de novo molecule design, the quantitative estimation of molecular synthetic accessibility (SA) has become a crucial factor for prioritizing the structures generated from ...
Baiqing Li, Hongming Chen
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International Journal of Control, 2021 For the purpose of precise mathematical modelling of chemical reaction networks, useful techniques for estimating their parameters from experimental data are necessary. In this manuscript, we propose a new parameter estimation method for enzymatic chemical reaction networks from time-series experimental data of reaction rates. The main idea is based on
Manvel Gasparyan +2 more
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RuleMonkey: software for stochastic simulation of rule-based models
BMC Bioinformatics, 2010 Background The system-level dynamics of many molecular interactions, particularly protein-protein interactions, can be conveniently represented using reaction rules, which can be specified using model-specification languages, such as the BioNetGen ...
Hlavacek William S +5 more
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CompLaB v1.0: a scalable pore-scale model for flow, biogeochemistry, microbial metabolism, and biofilm dynamics [PDF]
Geoscientific Model Development, 2023 Microbial activity and chemical reactions in porous media depend on the local conditions at the pore scale and can involve complex feedback with fluid flow and mass transport.
H. Jung, H. Jung, H.-S. Song, C. Meile
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Delays in Model Reduction of Chemical Reaction Networks
IFAC-PapersOnLine, 2018 Abstract A novel engineering model reduction method is proposed in this paper that can be applied to a chemical reaction network (CRN) with chains of linear reactions. The reduced model is a delayed CRN with possibly different delays but with less state variables than the original model.
György Lipták, Katalin M. Hangos
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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
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