Leonid Mirny (MIT)

Chromatin as a memory machine

One of the hallmarks of nuclear organization in eukaryotes is the spatial segregation of transcriptionally active (euchromatin) and inactive (heterochromatin) genomic regions. Recently we found that such compartmentalization is driven by affinity between heterochromatin regions (Falk et al Nature 2019) . Despite the widespread of such compartmentalized organization in nature, its functional roles remain elusive.

Here we examine the role of compartmentalization in the maintenance of epigenetic memory, i.e. maintenance of pattern of histone marks for hundreds of generations. We modeled joint dynamics of chromatin and histone marks: loss and spreading of marks, and refolding of chromosomes through the cell cycle. A surprinting analogy between the spreading of histone marks and the spreading of a disease in a pandemic helped to identify factors that provide robust memory. We further found a parallel between epigenetic memory and an associative memory in the neural network. Our analysis shows that operation of chromatin as a memory device requires enzyme limitation and spatial spreading of the marks in the dense and spatial segregated heterochromatin, suggesting a functional role for this hallmark of nuclear organization.

En version hybride, dans la salle de séminaire du LPTMC (couloir 13-12, 5ème, salle 5-23) et sur zoom:
 

Frédéric van Wijland (MSC, Université de Paris)

Multibody effects in active particle systems, and what working in large space dimension teaches us

Systems made of a large number of self-propelled particles live very far from equilibrium, which opens the door to unexpected collective behaviors, such as the motility-induced phase separation (MIPS). While a phenomenological understanding of such phenomena was  almost immediately available, microscopics-based approaches are usually difficult to conduct. By embedding these many-body systems in a large-dimensional space, some simplifications occur, and these allow us to pinpoint fundamental physical differences between a conventional equilibrium phase separation driven by pairwise forces, and MIPS, which had eluded phenomenological, coarse-grained, descriptions. These lie in the intrinsically  many-body nature of interactions in systems of active particles.

Work done in collaboration with Thibaut Arnoulx de Pirey

En version hybride, dans la salle de séminaire du LPTMC (couloir 13-12, 5ème, salle 5-23) et sur zoom:

https://us06web.zoom.us/j/88523294809?pwd=cnQ0QmQxUXYycVVPYVloS2FEMjhDdz09

ID de réunion : 885 2329 4809
Code secret : 613679

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