Small molecule reaction networks that model the ROS dynamics of the rhizosphere

2019 ◽  
Vol 55 (25) ◽  
pp. 3602-3605 ◽  
Author(s):  
Olga Taran ◽  
Vraj Patel ◽  
David G. Lynn
Keyword(s):  
Small Molecule ◽  
Reaction Diffusion ◽  
Reaction Networks ◽  
Form Complex ◽  
Molecule Reaction ◽  
Diffusion Networks

Molecules released by plants and bacteria form complex abiotic reaction diffusion networks that might regulate the ROS dynamics along the roots of the plants.

scholarly journals Compartmental and spatial rule-based modeling with Virtual Cell (VCell)

2017 ◽  
Author(s):  
M. L. Blinov ◽  
J. C. Schaff ◽  
D. Vasilescu ◽  
I. I. Moraru ◽  
J. E. Bloom ◽  
...  
Keyword(s):  
Reaction Diffusion ◽  
Molecular Complexes ◽  
Reaction Diffusion Equations ◽  
Reaction Networks ◽  
The Novel ◽  
Modeling Framework ◽  
Rule Based ◽  
Agent Based ◽  
Virtual Cell ◽  
Stochastic Simulator

AbstractIn rule-based modeling, molecular interactions are systematically specified in the form of reaction rules that serve as generators of reactions. This provides a way to account for all the potential molecular complexes and interactions among multivalent or multistate molecules. Recently, we introduced rule-based modeling into the Virtual Cell (VCell) modeling framework, permitting graphical specification of rules and merger of networks generated automatically (using the BioNetGen modeling engine) with hand-specified reaction networks. VCell provides a number of ordinary differential equation (ODE) and stochastic numerical solvers for single-compartment simulations of the kinetic systems derived from these networks, and agent-based network-free simulation of the rules. In this work, compartmental and spatial modeling of rule-based models has been implemented within VCell. To enable rule-based deterministic and stochastic spatial simulations and network-free agent-based compartmental simulations, the BioNetGen and NFSim engines were each modified to support compartments. In the new rule-based formalism, every reactant and product pattern and every reaction rule are assigned locations. We also introduce the novel rule-based concept of molecular anchors. This assures that any species that has a molecule anchored to a predefined compartment will remain in this compartment. Importantly, in addition to formulation of compartmental models, this now permits VCell users to seamlessly connect reaction networks derived from rules to explicit geometries to automatically generate a system of reaction-diffusion equations. These may then be simulated using either the VCell partial differential equations (PDE) deterministic solvers or the Smoldyn stochastic simulator.

scholarly journals Effective nonlocal kernels on reaction–diffusion networks

2021 ◽  
Vol 509 ◽  
pp. 110496
Author(s):  
Shin-Ichiro Ei ◽  
Hiroshi Ishii ◽  
Shigeru Kondo ◽  
Takashi Miura ◽  
Yoshitaro Tanaka
Keyword(s):  
Reaction Diffusion ◽  
Diffusion Networks
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