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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 ...
Do Motifs Reflect Evolved Function? – No Convergent Evolution of Genetic Regulatory Network Subgraph Topologies
(2008-10)
Methods that analyse the topological structure of networks have recently become quite popular. Whether motifs (subgraph patterns that occur more often than in randomized networks) have specific functions as elementary ...
Bio-logic: gene expression and the laws of combinatorial logic
(2008)
At the heart of the development of fertilized eggs into fully formed organisms and the adaptation of cells to changed conditions are genetic regulatory networks (GRNs). In higher multi-cellular organisms, signal selection ...
Genetic regulatory network models of biological clocks : evolutionary history matters
(2008)
We study the evolvability and dynamics of artificial genetic regulatory networks (GRNs), as active control systems, realizing simple models of biological clocks that have evolved to respond to periodic environmental stimuli ...