45 citations · 115 across the 13 of their papers we have counts for
14 papers
Test of the formal basis of Arrhenius law with heat capacities
Denis Michel
The exponential factor of Arrhenius satisfactorily quantifies the energetic restriction of chemical reactions but is still awaiting a rigorous basis. Assuming that the Arrhenius eq…
The basal level of gene expression associated with chromatin loosening shapes Waddington landscapes and controls cell differentiation
Gilles Flouriot, Charly Jehanno, Yann Le Page +3
The baseline level of transcription, which is variable and difficult to quantify, seriously complicates the normalization of comparative transcriptomic data, but its biological imp…
Reductionist approach to chemical rate constants using conditional energy probabilities
Denis Michel
Different rate theories yielded similar forms of rates constants consistent with the phenomenological Arrhenius law, although they were derived from various branches of physics inc…
Polylogarithmic equilibrium treatment of molecular aggregation and critical concentrations
Denis Michel, Philippe Ruelle
A full equilibrium treatment of molecular aggregation is presented for prototypes of 1D and 3D aggregates, with and without nucleation. By skipping complex kinetic parameters like…
A model of dynamic stability of H3K9me3 heterochromatin to explain the resistance to reprogramming of differentiated cells
Charly Jehanno, Gilles Flouriot, Pascale Le Goff +1
Despite their dynamic nature, certain chromatin marks must be maintained over the long term. This is particulary true for histone 3 lysine 9 (H3K9) trimethylation, that is involved…
Modeling generic aspects of ideal fibril formation
Denis Michel
Many different proteins self-aggregate into insoluble fibrils growing apically by reversible addition of elementary building blocks. But beyond this common principle, the modalitie…
Drawing a Waddington landscape to capture dynamic epigenetics
Floriane Nicol-Benoit, Pascale le Goff, Denis Michel
Epigenetics is most often reduced to chromatin marking in the current literature, whereas this notion was initially defined in a more general context. This restricted view ignores…
Conformational selection or induced fit? New insights from old principles
Denis Michel
A long standing debate in biochemistry is to determine whether the conformational changes observed during biomolecular interactions proceed through conformational selection (of pre…
The accuracy of biochemical interactions is ensured by endothermic stepwise kinetics
Denis Michel, Benjamin Boutin, Philippe Ruelle
The discerning behavior of living systems relies on accurate interactions selected from the lot of molecular collisions occurring in the cell. To ensure the reliability of interact…
A role for ATP-dependent chromatin remodeling in the hierarchical cooperativity between noninteracting transcription factors
Denis Michel
Chromatin remodeling machineries are abundant and diverse in eukaryotic cells. They have been involved in a variety of situations such as histone exchange and DNA repair, but their…
New treatments of density fluctuations and recurrence times for re-estimating Zermelo's paradox
Denis Michel
What is the probability that all the gas in a box accumulates in the same half of this box? Though amusing, this question underlies the fundamental problem of density fluctuations…
Kinetic approaches to lactose operon induction and bimodality
Denis Michel
The quasi-equilibrium approximation is acceptable when molecular interactions are fast enough compared to circuit dynamics, but is no longer allowed when cellular activities are go…
Seven competing ways to recover the Michaelis-Menten equation reveal the alternative approaches to steady state modeling
Denis Michel, Philippe Ruelle
The Michaelis-Menten enzymatic reaction is sufficient to perceive many subtleties of network modeling, including the concentration and time scales separations, the formal equivalen…
Simply conceiving the Arrhenius law and absolute kinetic constants using the geometric distribution
Denis Michel
Although first-order rate constants are basic ingredients of physical chemistry, biochemistry and systems modeling, their innermost nature is derived from complex physical chemistr…