Laboratoire Matière et Systèmes Complexes

Thomas Auger : Zero-Mode Waveguide detection of biomolecules transport through artificial nanopores and nuclear pore complexes

We have developed a novel single molecule optical observation method using a custom Zero Mode Waveguide setup to study the translocation of biopolymers through artificial and biological nanopores. Our work focuses on two aspects. First we monitored the flow driven injection of DNA molecules through solid state nanopores and showed that DNA starts translocating over a flow threshold independent of the pore radius, the DNA concentration and length. We demonstrate that the translocation is controlled by an energy barrier as proposed by the de Gennes - Brochard suction model. The height of the energy barrier can be modulated by functionalizing the nanopores with PEG-Thiols and we observe that the modulation is correlated to the length of the PEG polymers. More recently we adapted our setup to the study of transport through the nuclear pore complex (NPC) using extracted nuclear membranes from Xenopus Laevis oocytes. We aim at probing the conformation of unstructured proteins – the FG-Nucleoporins – crowding the central channel of the NPC by monitoring the free diffusion of small Dextran molecules (3kDa). We have been able to estimate the radius of the central pore of the NPC at a value between 4.4 nm and 4.9 nm in accordance with the literature. Following on this characterization, we want to study the effects of transporter molecules, which have a high affinity for the FG-Nups, on the central pore size and correlate it to the conformation of FG-Nups.

Tommy Dessup : Dynamics of nonlinear localized patterns in a quasi-one dimensional system of interacting particles

The systems of repulsively interacting particles confined in quasi-one dimensional geometry present a configurational phase transition known as the zigzag bifurcation. When the transverse confinement is smaller than a threshold the particles adopt a staggered row configuration. For short range interactions and periodic boundary conditions in the longitudinal direction, there exists an intermediate range of confinements for which the system presents phases coexistence, called bubble, with particles disposed in staggered row surrounded by particles in line.

We present a continuous nonlinear model developed in order to describe this bifurcation, the shape of these nonlinear instabilities and their dynamics characteristics.

In presence of thermal noise, these localized solutions remain stable and present an erratic motion. We show that this motion might be described as the free diffusion of a quasi-particle, with an effective mass that may be calculated from the solitary wave envelope of the localized pattern. Moreover we show that the discrete character of the system plays a key role on the bubble behavior at low temperature.

In a second part we consider systems with several localized patterns. We focus on their interactions and their reorganization toward an equilibrium configuration of a unique bubble. We show how the discrete character induces topological frustration effect: the bubble interaction is attractive for non-frustrated systems and repulsive for frustrated ones. Simulation results are compared to a theoretical expression developed in the framework of our model. Lastly we discuss the two processes used by the systems to reach their equilibrium configurations.