Dynamics of Living Matter

Thermodynamic and statistical physics

We use nonequilibrium thermodynamics and statistical mechanics to understand and model features of complex soft matter: interfaces, structure, rheology, phase transition...

Nonequilibrium interfacial thermodynamics

We analyze the local equilibrium of interfaces from the perspective of gauge transformations: the gauge is the choice for the location of the phase dividing surface. By evoking the gauge invariance of interfacial thermodynamic properties, we rigorously extend the validity of Clapeyron relations to nonequilibrium systems. We support our results using nonequilibrium molecular dynamics simulations of a liquid-gas interface.

Soft matter modeling

We model soft matter as a dispersion of particles, that are made of a core and a corona. The cores interact through conservative forces, while the coronae overlap to form temporary interactions, typically of entropic origin. This model is very efficient in accounting for the transient forces found in entangled polymers, for example. Using the Generic framework of nonequilibrium thermodynamics, we notably derive the stress tensor for this rheological model.

Quantifying microstructural heterogeneity

We derive unbiased estimators that quantify the micrometric heterogeneity of complex matter, as measured by the multiple particle tracking technique. This method provides new insights on how soft matter is organized at the mesoscale, and has recently been applied to probe clay gelation (Rich et al., 2011) and hydrogel formation (Aufderhorst-Roberts et al., 2012).

Entropic interaction

Depletion interaction is an entropic force that can drive phase transition in colloidal mixtures. The case of spherical particles bathing in a solution of Brownian rod-like polymers is archetypical. We derive the analytical expression of this entropic interaction potential between the spheres for this case.

Experimental methods

We develop new and simple experimental methods to probe the mechanical properties of soft matter, biological and synthetic, at "unusual" scales.

Particle tracking microrheology

We use digital video microscopy to measure, with nanometer precision, the Brownian motion of hundred micrometric probes embedded in a complex fluid. Statistics calculated from the trajectories can then be used to measure the micromechanics of the material. We quantified the propagation of detector artifacts on these statistics, to provide multifold improvements in their resolution.

Biological tissue mechanical test

We invented a new technique to determine the tensile properties of biological tissues at the mesoscale. The procedure uses a calibrated magnetic interaction between a steel bead, attached to the sample, and a permanent magnet to apply uniaxial tensile force. A simple video assay monitors the sample extension. The force applied falls in the micro- and milli-Newton range, along with displacements in the sub-millimetric range, particularly suitable for embryonic tissues.

Multiscale biophysics

We assess forces and mechanical properties in biological systems, at various length scales, and we ask how these forces influence the structure, shape and function of the organs.

Mechanoresponsive protein fibers

We developed a coarse-grained numerical model of fibronectin chains that captures the conformational changes of their repeat units upon extension. We studied the tensile properties of the chains' assembly into bundled fibers, and proved the essential role of the cryptic interactions, which are activated only by unfolded repeats, in enhancing mechanical toughening.

Self-assembly of peptide matrix

The fibrous networks formed from peptide self-assembly are very efficient gel scaffolds for cell growth and tissue regeneration. We tracked the motion of embedded microprobes to measure the kinetics of the hydrogel formation. We showed that the time of self-assembly can be reduced from hours to minutes, only by tuning the effective charge of the peptides. We further derived a simple electrostatic model that explains these results.

Physics of blood occlusion

When red blood cells move in file through narrow capillaries in the microcirculation, they deform as they flow. Loss of cell deformability in pathological processes (e.g. sickle cell disease, malaria) severely restricts the blood flow. We performed novel experiments on the flow of a red blood cell in a glass capillary to isolate and model the physics of blood occlusion over a wide range of driving pressure, confinement and cell deformability.

Morphogenesis

The pattern in which intestines are folded is characteristic of species. Using developmental and biophysical experiments, along with theory, computational and rubber analogs, we showed that the reproducible form of the gut looping is governed by simple mechanics of the growing tissues during embryogenesis. The gut tube grows faster than the muscular sheet that anchors it to the body, thus forcing the intestine to loop.