Research
Evolution / Population dynamics
Quantifying fitness, selection and survival is a fundamental step in any description of evolution. However, previous definitions of these notions often rely on specific dynamical models. Instead, we use different samplings of the lineages in population trees of dividing organisms, which capture the bias between the population and the single cell levels, to obtain a model-free description of evolution. The results following from this approach are interpreted within the frameworks of stochastic thermodynamics and linear response theory, and provide universal constraints on growth, fitness, selection and survival. Although our research is framed for cell colonies, we hope to find applications in species/gene trees.
Related publiations:
- Cell Lineage Statistics with Incomplete Population Trees, A. Genthon, T. Nozoe, L. Peliti, D. Lacoste, PRX Life (2023)
- Universal constraints on selection strength in lineage trees, A. Genthon, D. Lacoste, PRR (2021)
- Fluctuation relations and fitness landscapes of growing cell populations, A. Genthon, D. Lacoste, Sci. Rep. (2020)
- Linking lineage and population observables in biological branching processes, R. Garcia-Garcia, A. Genthon, D. Lacoste, PRE (2019)
Cell size distribution and cell size control
Cell size homeostasis can only be achieved by specific mechanisms of cell size control, that regulate growth and division. We investigate the effect of the randomness of these mechanisms (target division size, elongation rate, volume asymmetry between sister cells) on the cell size distribution. Because they are correlated with reproductive success, these sources of stochasticity imply biases between the population and lineage distributions.
Related publiations:
- Analytical cell size distribution: lineage-population bias and parameter inference, A. Genthon, J. R. Soc. Interface. (2022)
Physics of DNA melting
We study the melting of a defect basepair and its neighbours in an otherwise homogeneous DNA (only one type of basepair). The defect locally modifies the binding (Watson-Crick) and stacking (nearest neighbors) energies, as caused by basepair mismatches or fluorescent labels attached to the DNA, for example. The analytical solution informs on the scope of the perturbation induced by the defect and on the nature of the melting phase transition.
Related publiations:
- Equilibrium melting probabilities of a DNA molecule with a defect: An exact solution of the Poland–Scheraga model, A. Genthon, A. Dvirnas, T. Ambjörnsson, J. Chem. Phys. (2023)
Thermodynamics of cell division
To study the thermodynamics of cell division, which is an absolutely irreversible process, we split division into two sub-processes: branching, by which a cell duplicates, and resetting, by which the properties of newborn cells are reset to new values. Both processes modify the energy and the entropy of the system, on the basis of which we propose a measure of efficiency for cell division, that is evaluated for different models of cell size control.
Related publiations:
- Branching processes with resetting as a model for cell division, A. Genthon, R. Garcia-Garcia, D. Lacoste, J. Phys. A: Math. Theor. (2022)