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Symmetry structure in discrete models of biochemical systems : natural subsystems and the weak control hierarchy in a new model of computation driven by interactions
(2015-07-28)
Interaction Computing (IC) is inspired by the observation that cell metabolic/regulatory systems construct order dynamically, through constrained interactions between their components and based on a wide range of possible ...
Exploring the concept of interaction computing through the discrete algebraic analysis of the Belousov-Zhabotinsky reaction
(2013-05)
Interaction computing (IC) aims to map the properties of integrable low-dimensional non-linear dynamical systems to the discrete domain of finite-state automata in an attempt to reproduce in software the self-organizing ...
BIOMICS Project : Biological and Mathematical Basis of Interaction Computing
(2012)
The main idea that led us to propose this project is inspired by the observation that cell metabolic/regulatory systems are able to self-organise and/or construct order dynamically, through random interactions between their ...
Algebraic analysis of the computation in the Belousov-Zhabotinsky reaction
(Springer Nature, 2012)
We analyse two very simple Petri nets inspired by the Oregonator model of the Belousov-Zhabotinsky reaction using our stochastic Petri net simulator. We then perform the Krohn-Rhodes holonomy decomposition of the automata ...
Stochastic model of template-directed elongation processes in biology
(2010)
We present a novel modular, stochastic model for biological template-based linear chain elongation processes. In this model, elongation complexes (ECs; DNA polymerase, RNA polymerase, or ribosomes associated with nascent ...
Genetic algorithms and their application to in silico evolution of genetic regulatory networks
(2010)
A genetic algorithm (GA) is a procedure that mimics processes occurring in Darwinian evolution to solve computational problems. A GA introduces variation through "mutation" and "recombination" in a "population" of possible ...