Hadrien Vroylandt (Institut des Sciences du Calcul et des Données, Sorbonne Université)

Learning the dynamics of systems with memory : Generalized Langevin equations

Generalized Langevin equations with non-linear forces and memory kernels are commonly used to describe the effective dynamics of coarse-grained variables in molecular dynamics. Such reduced dynamics play an essential role in the study of a broad class of processes, ranging from chemical reactions in solution to conformational changes in biomolecules or phase transitions in condensed matter systems. I will first discuss the derivation of the generalized Langevin equations, emphasizing the need for memory in the effective dynamics due to the lack of a proper separation of time scales. Then, I will turn on the inference of such generalized Langevin equations from observed trajectories, using a maximum likelihood approach. This data-driven approach provides a reduced dynamical model for collective variables, enabling the accurate sampling of their long-time dynamical properties at a computational cost drastically reduced with respect to all-atom numerical simulations. I will illustrate the potential of this method on several model systems, both in and out of equilibrium.

En visioconférence par zoom
Lien : https://us06web.zoom.us/j/81533150574?pwd=NlM1ZlJvUTQvZUxpVmV6QWdMbmlLQT09
Meeting ID: 815 3315 0574
Passcode: 336254

David Dean (LOMA, Université de Bordeaux)

Non-monotonic Casimir forces

In this talk I will discuss two examples of systems where thermal or quantum fluctuations lead to fluctuation induced forces which have a non-monotonic behavior that can lead to strong metastability. The first example corresponds to a field theory with higher derivative interactions (examples arise in non-local electrostatics and polymer physics). The second comes from free fermionic systems in the presence of impurities. Despite corresponding to drastically different physics, the two examples show remarkably similar Casimir force phenomenology.

En version hybride en personne dans la salle de séminaire habituelle (couloir 12-13, 5ème, salle 5-23) et en visioconférence par zoom
https://us06web.zoom.us/j/89465455986?pwd=cDVTVjAvclNzNlIzNDdpaUhoU1Vhdz09
Meeting ID: 894 6545 5986
Passcode: 355776

Aurélien Grabsch (LPTMC)

Generalised Density Profiles in Single-File Systems

Single-file transport, where particles diffuse in narrow channels while not overtaking each other, is a fundamental model for the tracer subdiffusion observed in confined systems, such as zeolites or carbon nanotubes. This anomalous behavior originates from strong bath-tracer correlations in 1D, which we characterise in this talk through Generalised Density Profiles (GDPs). These GDPs have however remained elusive, because they involve an infinite hierarchy of equations. Here, for the Symmetric Exclusion Process, a paradigmatic model of single-file diffusion, we break the hierarchy and unveil a closed equation satisfied by these correlations, which we solve. Beyond quantifying the correlations, the central role of this equation as a novel tool for interacting particle systems will be further demonstrated by showing that it applies to out-of equilibrium situations, other observables and other representative single-file systems.

Refs:
* Generalized Correlation Profiles in Single-File Systems
  Alexis Poncet, Aurélien Grabsch, Pierre Illien, Olivier Bénichou
  Phys. Rev. Lett. 127, 220601 (2021), arXiv:2103.13083
* Closing and Solving the Hierarchy for Large Deviations and Spatial Correlations in Single-File Diffusion
  Aurélien Grabsch, Alexis Poncet, Pierre Rizkallah, Pierre Illien, Olivier Bénichou
  arXiv:2110.09269

En visioconférence par zoom
https://us06web.zoom.us/j/83490021896?pwd=WUhkRkVOOUN1b3VhTE1Ra3lqMzNsUT09
Meeting ID: 834 9002 1896
Passcode: 342955

Scolari Vittore (Institut Curie)

Forces shaping chromatin in the nucleus

The physics of genome dynamics requires innovative out-of-equilibrium approaches because the cell nucleus, from the most basic chemical reactions to evolutionary timescales of billions of years, strives to counteract disorder in order to be healthy, consuming energy, being alive. My objective is to develop a physical theory able to describe intranuclear dynamics, with the ambition of reaching a quantitative understanding of the two essential processes of gene regulation and DNA recombination. In particular, I investigate: (i) how 3D chromosome conformation is shaped by specific biological processes. Particularly loop extrusion and the formation of foci – or phases – for heterochromatin and transcription, and (ii) the fundamental implications of thee mechanisms on control and reliability of the biological processes of transcriptional induction, gene silencing, and evolution. In this talk I will present my original approach to simulate loop extrusion, an active process central in regulating the shape of chromatin in vivo. The “gold standard” currently uses molecular dynamics simulations: while very flexible, this limits our possibility (i) to explore the parameter space in an efficient manner and (ii) to dissect the observed effects under the lenses of a coherent analytical theory. I will show my original approach that exploits the analytical solution of the Einstein-Smoluchowski equation for the Rouse model affected by the action of extruders simulated in 1D. The resulting probability distributions highlight the hallmarks of the out-of-equilibrium processes on chromatin conformation observed in vivo by experiments. Finally, this approach permits the definition of the Gibbs entropy of chromosome conformation. I will show how the application of this concept to simplified toy-models increases our analytical understanding of the loop extrusion process. Finally, I will present my future scientific plans.