Influence of Dispersion Interactions on the Polymorphic Stability of Crystalline Oxides.

The accurate determination of relative phase stabilities using DFT methods is a significant challenge when some of these can vary by only a few kJ/mol. Here, we demonstrate that for a selection of oxides (TiO, MnO, and ZnO) the inclusion of dispersion interactions, accomplished using the DFT-D3 correction scheme, allows for the correct ordering and an improved calculation of the energy differences between polymorphic phases. The energetic correction provided is of the same order of magnitude as the energy difference between phases.

Positive and negative cycles in Boolean networks.

We review and discuss some results about the influence of positive and negative feedback cycles in asynchronous Boolean networks. These results merge several ideas of Thomas: positive and negative feedback cycles have been largely emphasized by Thomas, through the so called Thomas' rules, and asynchronous Boolean networks have been introduced by Thomas as a model for the dynamics of gene networks, which is nowadays very popular.

Modelization of the regulation of protein synthesis following fertilization in sea urchin shows requirement of two processes: a destabilization of eIF4E:4E-BP complex and a great stimulation of the 4E-BP-degradation mechanism, both rapamycin-sensitive.

Fertilization of sea urchin eggs involves an increase in protein synthesis associated with a decrease in the amount of the translation initiation inhibitor 4E-BP. A highly simple reaction model for the regulation of protein synthesis was built and was used to simulate the physiological changes in the total 4E-BP amount observed during time after fertilization. Our study evidenced that two changes occurring at fertilization are necessary to fit with experimental data.

On circuit functionality in Boolean networks.

It has been proved, for several classes of continuous and discrete dynamical systems, that the presence of a positive (resp. negative) circuit in the interaction graph of a system is a necessary condition for the presence of multiple stable states (resp. a cyclic attractor).

Boolean models of biosurfactants production in Pseudomonas fluorescens.

Cyclolipopeptides (CLPs) are biosurfactants produced by numerous Pseudomonas fluorescens strains. CLP production is known to be regulated at least by the GacA/GacS two-component pathway, but the full regulatory network is yet largely unknown. In the clinical strain MFN1032, CLP production is abolished by a mutation in the phospholipase C gene (plcC) and not restored by plcC complementation.

Stable periodicity and negative circuits in differential systems.

We provide a counter-example to a conjecture of René Thomas on the relationship between negative feedback circuits and stable periodicity in ordinary differential equation systems (Kaufman et al. in J Theor Biol 248:675-685, 2007). We also prove a weak version of this conjecture by using a theorem of Snoussi.

Epigenesis and dynamic similarity in two regulatory networks in Pseudomonas aeruginosa.

Mucoidy and cytotoxicity arise from two independent modifications of the phenotype of the bacterium Pseudomonas aeruginosa that contribute to the mortality and morbidity of cystic fibrosis. We show that, even though the transcriptional regulatory networks controlling both processes are quite different from a molecular or mechanistic point of view, they may be identical from a dynamic point of view: epigenesis may in both cases be the cause of the acquisition of these new phenotypes. This was highlighted by the identity of formal graphs modelling these networks.

Application of formal methods to biological regulatory networks: extending Thomas' asynchronous logical approach with temporal logic.

Based on the discrete definition of biological regulatory networks developed by René Thomas, we provide a computer science formal approach to treat temporal properties of biological regulatory networks, expressed in computational tree logic. It is then possible to build all the models satisfying a set of given temporal properties. Our approach is illustrated with the mucus production in Pseudomonas aeruginosa.