Nanoparticules de type « cage » : applications pour lutter contre le cancer et les infections résistantes au traitement

Ruxandra Gref (ISMO, Université Paris-Sud)

Deux exemples de vecteurs de médicaments élaborés par une « chimie douce » (sans solvant) seront présentés : i) les nanoparticules hybrides organiques-inorganiques (metal-organic frameworks ou MOFs), qui sont des assemblages supramoléculaires cristallins hautement poreux, et ii) les nanoparticules à base de cyclodextrines, molécules « cage ». Avantageusement, ces nanoparticules sont capables d’encapsuler des quantités importantes de molécules thérapeutiques de nature chimique variée par simple imprégnation dans un milieu aqueux. La surface de ces vecteurs a été modifiée avec des éléments de reconnaissance spécifiques afin de moduler l’interaction des nanoparticules avec le milieu vivant et d’accroitre l’internalisation de celles-ci dans les cellules cible (cellules cancéreuses ou cellules infectées avec le VIH ou des bactéries). Finalement, des exemples seront présentés ou la libération des molécules thérapeutiques se fait « sur demande » suite à l’application d’un stimulus externe. Les applications de ces travaux se situent dans le domaine du traitement du cancer et des infections résistantes au traitement.

Quasi-bound states in periodically driven scattering

Haggai Landa (LPTMS)

Soutenance HDR Dmitry Petrov

Workshop on Nuclei, atoms, molecules: Few-body problem and beyond

One solid, two glasses

Beatriz Seoane Bartolome (LPT-ENS Paris)

Inferring anomalous diffusion from single particle trajectories

Denis Grebenkov (PMC, École polytechnique)

SPECIAL LOCATION

Transport of macromolecules, organelles and vesicles in living cells is a very complicated process that essentially determines and controls many biochemical reactions, growth and functioning of cells. The passive thermal diffusion through the overcrowded cytoplasm is combined with the active transport by motor proteins attached to microtubules. This intricate mechanism results in anomalous diffusions that found abundant experimental evidences but no consensus on the physical mechanism and the appropriate mathematical model is achieved so far. Single-particle tracking (SPT) experiments survey random trajectories of individual tracers inside living cells and can thus provide the missing information on the intracellular transport in order to discriminate between different physical mechanisms and to identify the appropriate theoretical model of anomalous diffusion. In SPT, an ensemble average of the quantities of interest (e.g., diffusivity, viscosity, first passage times, etc.) is often unavailable or even undesired, as tracers move in spatially heterogeneous and time evolving media such as living cells. One faces therefore a challenging problem of inferring dynamical, structural and functional properties of living cells from a limited (small) number of individual random realizations of an unknown stochastic process.

After a short introduction to theoretical aspects of the intracellular transport, we discuss the recent progress onto probing ergodicity of the tracer dynamics from a single particle trajectory. The proposed estimators are first investigated for several models of anomalous diffusion. In the case of nonergodic continuous time random walks, we show analytically that both estimators do not vanish even for infinitely long trajectories. The estimators are then applied to two sets of earlier published trajectories: mRNA molecules inside live E. coli cells and Kv2.1 potassium channels in the plasma membrane. These tests suggest that the former set exhibits ergodic behavior while the latter reveals both ergodic and nonergodic features.

Elisabeth Agoritsas (Université Grenoble-Alpes)

Jean-Marie Stephan (PKS-MPG Dresden)

Mechanics of B cell response

Paolo Pierobon (Institut Curie, Paris)

B lymphocytes are the antibodies producing cells and therefore essential effectors of adaptive immunity. In vivo, their activation is mostly triggered by the engagement of their B cell receptor (BCR) with antigens exposed at the surface of neighbouring antigen presenting cells. This leads to the formation of a signalling platform, the immune synapse, where cytoskeleton rearrangement are essential for the antigen extraction, internalization and processing. While it has been shown that on a hard substrate the cell follows a dynamics of spreading and contraction, this has never been investigated on substrates with rigidity close to the physiological one. We measure for the first time the forces produced by B cells on deformable antigen coated surfaces (traction force microscopy) and show that these forces are contractile, specifically induced by BCR activation and Myosin II dependent. We characterize the contractile dynamics of the cell and argue that in generating pulling forces, Myosin II plays a crucial role in antigen gathering and internalization. These results open interesting perspectives on the role of mechanics in the acquisition of specific antigen and more generally on receptor internalization.

Manon Michel (LPS-ENS)

Giacomo Gradenigo (Grenoble-Alpes)

Assessment of optimal parameters for deep optogenetic stimulations in non human primate

Frédéric Pain (IMNC, Université Paris-Sud)

SPECIAL LOCATION (next door from the usual one)

Optogenetics has become ubiquitous in fundamental neuroscience labs as a very powerful tool to unravel brain networks connectivity and cellular mechanisms. Yet, its clinical translation requires a careful assessment of the inocuity of repeated and sustained high power light stimulations. In a preliminary studies to translational research in the field deep brain stimulation for Parkinson's disease we have studied in vivo in anesthetized rats the potential damages and non-physiological effects produced by high power optical neurostimulation in typical optogenetics experiments.2D Maps of light distribution and temperature increase were recorded in wild type anesthetized rats brains for relevant optical stimulation protocols used in optogenetics. The spatial profile of light distribution and heat were correlated and demonstrated as expected a rapid attenuation with distance to the fiber. Temperature increase remains below physiological changes for stimulations up to 400mW/mm². I will present optogenetics issues in a clinical translational context.

GW150914 : la naissance de l'astronomie des ondes gravitationnelles

Patrice Hello (LAL, Université Paris Sud)

Conformal invariance in statistical and quantum physics

Shaping a fly wing

Franck Jülicher (MPI-PKS Dresden)

A fundamental question in Biology is to understand the morphogenetic processes by which an organism of complex shape forms from a fertilized egg. This morphogenesis involves the dynamic remodeling of tissues consisting of many cells that grow and divide. The fly wing is an important model system for the study of multicellular dynamics during tissue morphogenesis. During pupal stages, the early fly wing undergoes a spectacular dynamic reorganization that involves cell flows, cell divisions and cell shape changes. This dynamic process generates the final shape of the wing. We characterize tissue remodeling by the contributions of specific cellular processes such as cell shape changes and cell neighbor exchanges to macroscopic shear at different times. We discuss the dynamics and the mechanics of this tissue using theoretical approaches that capture the essential physics of tissue remodeling. Our work suggests that local tissue contraction together with anisotropic active processes drive tissue remodeling in the fly wing. We show that mechanical boundary conditions play a key role in determining the final tissue shape.

Acrobatics of liquid ropes

Neil Ribe (FAST, Université Paris-Sud)

Integrable models of directed polymers on the square lattice

Thimothée Thiery (LPT ENS Paris)

Fluctuation theorem for entropy production of a partial system in the weak coupling limit

Sanjib Sabhapandit (Raman Research Institute, Bangalore, India)

Thermalization with Chemical Potentials, and Higher Spin Black Holes

Ritam Sinha (Tata Institute of Fundamental Research, Mumbai)

Premier temps d'atteinte de la chambre de Weyl par le processus de Dunkl radial

Nizar Demni (Institut de Recherches Mathématiques de Rennes, Université de Rennes)

SEMINAR CANCELLED

Scattering theory of walking droplets in the presence of obstacles

Rémy Dubertrand (Université de Liège, Belgique)

Modeling of dynamical phase transitions in electronic systems induced by ultra-fast optical pumping

Serguei Brazovskii (LPTMS)

Exact many-body dynamics of a harmonically quenched Tonks-Giradeau gas at finite temperature

Yasar ATAS (University of Queensland, Brisbane, Australia)

Ultracold quantum gases offer a fascinating and remarkably insightful playground for exploring and understanding the fundamentals of out-of-equilibrium behaviour of quantum matter. Experimental systems whose non-equilibrium dynamics can be described by exactly solvable models of quantum many-body theory play a particularly important role.  A paradigmatic example in this realm is the Tonks-Girardeau (TG) gas  of strongly interacting bosons, previously treated only for zero-temperature dynamics.

In this talk, I will present an exact finite temperature dynamical theory of a harmonically trapped TG gas, and apply it to the problem of breathing-mode oscillations after a sudden confinement quench.  The method is based on the Fredholm determinant expression of the density matrix at finite temperature and provides a straightforward and efficient technique to compute finite temperature properties of TG. I will identify physical regimes for observing a phenomenon of frequency doubling in the oscillations of the momentum distribution of the gas.  Exact results will be compared to a finite-temperature hydrodynamic approach based on local density approximation with the frequency quasi-doubling phenomena surprisingly well captured. The exact dynamical theory developed opens the way to solving finite-temperature problems involving anharmonic traps, as well as arbitrary quench protocols of the trapping potential.

Magnetic field properties of itinerant electrons in a quasicrystal

Jean-Noël Fuch (LPS, Univeristé Paris-Sud & LPTMC, Université Paris 6)

Recent numerical insights on the many-body localization problem

Nicolas Laflorencie (Laboratoire de Physique Théorique, Université Paul Sabatier, Toulouse)

Random walks in confined geometry: convex hull and cover times

Marie Chupeau (LPTMC, UPMC, Paris)

Mixed order phase transitions: from DNA denaturation to jamming processes

David Mukamel (Weizmann Institute of Science, Israël)

Dissipation-assisted prethermalization in long-range interacting atomic ensembles

Giovanna Morigi (Universität des Saarlandes, Allemagne)

We theoretically characterize the semiclassical dynamics of an ensemble of atoms after a sudden quench across a driven-dissipative second-order phase transition. The atoms are driven by a laser and interact via conservative and dissipative long-range forces mediated by the photons of a single- mode cavity. These forces can cool the motion and, above a threshold value of the laser intensity, induce spatial ordering. The relaxation dynamics exhibits a long prethermalizing behaviour which is first solely dominated by coherent long-range forces, and then by their interplay with dissipation. Remarkably, this final stage is orders of magnitude slower and exhibits correlations which are established by spatially-correlated noise and which go beyond mean-field. This behaviour challenges the common understanding of the role of dissipation in the relaxation dynamics. It further implies that cavity cooling of an atomic ensemble into the selforganized phase can require longer time scales than the typical duration of an experiment.

Many Body Localization Transition : level statistics and entanglement entropy

Cécile Monthus (IPhT, CEA, Saclay)

Active Composite Cell Surface - local control of clustering and sorting

Madan Rao (Raman Research Institute & National Centre for Biological Sciences-TIFR, Bangalore)

The surface of a living cell needs to regulate and control its local composition in a variety of contexts such as endocytosis and signalling. We have shown that many cell surface molecules are organised at multiple scales by their coupling to a thin cortical actomyosin layer, which actively drives local cell membrane composition and shape. This includes both transmembrane proteins and lipid anchored proteins, such as GPI-anchored proteins. Crucial to this engagement is the spontaneous emergence of localized contractile platforms in the 2dim active cortical fluid. Both the nanoscale clustering and the mesoscale segregation display the unique signatures of activity. We have recently recapitulated many of these effects in a minimal reconstituted system. I will end by discussing potential implications of this active composite cell surface for the processing of cellular information.

Probing eigenfunction nonorthogonality by parametric shifts of resonance widths

Dmitry Savin (Brunel University, Uxbridge, UK)

High-Speed Atomic Force Microscopy: The dawn of dynamic structural biochemistry

Simon Scheuring (INSERM & Aix-Marseille Université)

The advent of high-speed atomic force microscopy (HS-AFM [1]) has opened a novel research field for the dynamic analysis of single bio-molecules: Molecular motor dynamics [2,3] membrane protein diffusion [4], assembly [5] and conformational changes [6] could be directly visualized. Further developments for buffer exchange [7] and temperature control [8] during HS-AFM operation provide breakthroughs towards the performance of dynamic structural biochemistry using HS-AFM.

[1] Ando et al., Chem Rev. 2014 Mar 26;114(6):3120-88.
[2] Kodera et al., Nature. 2010 Nov 4;468(7320):72-6.
[3] Uchihashi et al., Science. 2011 Aug 5;333(6043):755-8.
[4] Casuso et al., Nat Nanotechnol. 2012 Aug;7(8):525-9.
[5] Chiaruttini et al., Cell. 2015 Nov 5;163(4):866-79.
[6] Ruan et al., 2016, in preparation
[7] Miyagi et al., Nat Nanotechnol. 2016, in press
[8] Takahashi et al., 2016, in preparation

Finite temperature free fermions and the Kardar-Parisi-Zhang equation at finite time

Grégory Schehr (LPTMS, Université Paris-Sud)

Probing protein interactions on a microtubule bench by fluorescence microscopy: Application to YB-1, a mRNA-binding protein

David Pastré (Université d'Évry)

A typical procedure adopted by biologists to analyze protein interactions is to take advantage of the high throughput capability of the two hybrid system, generally in yeast, or that of the combination of affinity purification with mass spectrometry to obtain an exhaustive list of potential partners for a protein of interest. However, these assays require cell lysis, antibodies and adsorption onto non physiological substrates leading to false positives and false negatives. There is therefore a need to control the relevance of the proposed interactions in a context closer to native conditions, such as in living mammalian cells. To that end, novel methods are currently developed to provide a better view on protein interactions. In line with this, we have proposed a novel technology to detect and quantify direct or indirect protein interactions by fluorescence microscopy in living mammalian cells using microtubules as platforms. Microtubules are micrometer-long rigid cylinders of about 25 nm in diameter that are present in the cytoplasm of all eukaryotic cells. Due to their geometry, they provide an ideal surface to probe molecular interactions by fluorescence microscopy. As a proof of concept, we used microtubules to probe the interactions between mRNA-binding proteins like YB-1 in the cytoplasm.

Active contraction in biological fiber networks

Large-scale force generation is essential for biological functions such as cell motility, embryonic development, wound healing and muscle contraction. In these processes, forces generated at the molecular level by motor proteins are transmitted by disordered fiber networks, resulting in large-scale active stresses.  While fiber networks are well characterized macroscopically, this stress generation by microscopic active units is not well understood. In this Thesis, I present a comprehensive theoretical and numerical study of force transmission in elastic fiber networks. I show that the linear, small-force response of the networks is remarkably simple, as the macroscopic active stress depends only on the geometry of the force-exerting unit. In contrast, as non-linear buckling occurs around these units, local active forces are rectified towards isotropic contraction, making the local geometry of force exertion irrelevant. This emergent contractility is amplified by non-linear force transmission through the network. This stress amplification is reinforced by the networks' disordered nature, but saturates for high densities of active units. Our predictions are quantitatively consistent with experiments on reconstituted tissues and actomyosin networks, and that they shed light on the role of the network microstructure in shaping active stresses in cells and tissue.

Elastoplastic models for amorphous plasticity

Jean-Louis Barrat (Université Joseph Fourier, Grenoble)

I will present our current understanding, based on microscopic simulations and experiments, of the elementary mechanisms that govern the deformation and flow of amorphous materials. I will show how these mechanisms can be incorporated into  simple lattice models governed by long range elastic interactions, discuss the mean field analysis of these models as well as fluctuation related issues such as the  statistics of avalanche like events.

References:

• Modeling deformation and flow of disordered materials, J-L. Barrat, J.J. de Pablo, MRS Bulletin 32, 941 (2007)
• Driving rate dependence of avalanches statistics and shapes at the yielding transition, C. Liu, E. Ferrero, F. Puosi, J-L. Barrat, K. Martens, PRL 116 065201 (2016)
• On the relevance of disorder in athermal amorphous materials under shear, E. Agoritsas, E. Bertin, K. Martens, J-L. Barrat EPJE 38 15071 (2015)
• Rheology of athermal amorphous solids: Revisiting simplified scenarios and the concept of mechanical noise temperature, A. Nicolas, K. Martens, J-L. Barrat EPL 107 44003 (2014)

Metastability transition in genome evolution and population structure of bacterial species

Purushottam Dixit (Columbia University, US)

Ergodic transition on disordered random regular graph

Vladimir Kravtsov (ICTP, Trieste, Italy)

Inferring interaction partners from protein sequences

Anne-Florence Bitbol (Laboratoire Jean Perrin, UPMC)

SPECIAL LOCATION (due to renovation work at LPS)

Specific protein-protein interactions play crucial roles in the stability of multi-protein complexes and in signal transduction. Thus, mapping these interactions is key to a systems-level understanding of cells. However, systematic experimental identification of protein interaction partners is still challenging, while a large and rapidly growing amount of sequence data is now available. Is it possible to identify which proteins interact just from their sequences? We propose an approach based on sequence covariation, building on methods used with success to predict the three-dimensional structures of proteins from sequences alone. Our method identifies specific interaction partners with high accuracy among the members of two ubiquitous prokaryotic protein families, and paves the way to identifying novel protein-protein interactions directly from sequence data.

Mathematical modelling of limit order books

Frédéric Abergel (Laboratoire MICS, Ecole Centrale de Paris)

&

Nonparametric statistics from cumulative sample sums

Damien Chalet (Laboratoire MICS, Ecole Centrale de Paris)

1) Stefano Spigler : "Distribution of avalanches in perturbed disordered systems"

2) Pierre Ronceray : "Suppression of crystalline order by competing liquid structures"

Coherently driven 2-component Bose gases

Alessio Recati (Università di Trento, Italia)

Universality in the Entanglement and Localization of Strongly Chaotic Subsystems

Steven Tomsovic (Washington State University, USA)

Fluctuations in in vivo reactive systems.

Hélène Berthoumieux (LPTMC - Université Pierre & Marie Curie, Paris)

SPECIAL LOCATION (due to renovation work at LPS)

For a chemist, a living cell is a reactive system in which the concentrations of biomolecules are not determined by the thermodynamics but are controlled by energy sources maintaining the system in an out-of-equilibrium state. Chemical reaction networks are thus perturbed by a thermal noise and the fluctuations of these energy sources. Theoretical and experimental studies have shown that the fluctuations of in vivo systems break the fluctuation-dissipation theorem, which is a result of statistical physics at equilibrium. One can thus ask what information is contained in the correlation functions of protein concentrations and how they relate to the response of the reactive network to a perturbation. Answers to these questions are of prime importance to extract meaningful parameters from the in vivo fluorescence correlation spectroscopy data. Here, we present a theoretical study of the fluctuations of the concentration of a reactive species involved in a cyclic network that is in a non-equilibrium steady state perturbed by a noisy force, taking into account both the breaking of detailed balance and extrinsic noises that are known to be important in a cell.

AdS/CFT and condensed matter systems

Giuseppe Policastro (LPT-ENS, Paris)

 In this talk I will give an introduction to the idea of the holographic correspondence and some of its applications. In recent years holography has been shown to be a very useful tool to get theoretical insight into systems that can not be studied by more conventional methods, typically because there is no small expansion parameter; such systems include the QCD quark/gluon plasma, high-temperature superconductors, condensed matter systems in the vicinity of a quantum critical point, and strongly correlated electron systems (non-Fermi liquids). I will discuss how, while it is usually not possible to match any given realistic system with a corresponding holographic description, the method is useful for deriving results of a general nature. I will highlight the main successes of the method and some of the open questions.

Weinberg representation, coherent and anticoherent spin states

Olivier Giraud (LPTMS)

Tradeoffs between fast growth and adaptability shape microbial phenotypes

Markus Basan (ETH Zurich, Switzerland & Harvard University, USA)

SPECIAL LOCATION (due to renovation work at LPS)

Microorganisms exhibit a striking diversity of phenotypes in different conditions. Changes in growth rates are accompanied by large variations in metabolic strategies, gene expression and cell size. However, the molecular basis and underlying rationale of many of these complex patterns remains poorly understood. We illustrate how a quantitative approach, based on establishing empirical relations between cellular phenotypes, can help to elucidate such questions by focusing on three long-standing biological problems: the origin of overflow metabolism, the control of cell size and finally we provide an outlook on the emergence of severe, multi-hour lag phases. Coarse-grained models yield a quantitative and predictive understanding of phenotypic patterns under environmental as well as genetic perturbations and can even shed light on underlying molecular mechanisms. A common theme that emerges from these seemingly diverse questions is the existence of fundamental tradeoffs between fast growth and the ability to swiftly adapt to environmental changes or stress conditions.

Interacting gases with a synthetic gauge field in the synthetic dimension

Leonardo Mazza (Ecole Normale Supérieure / PSL Research University, CNRS)

Synthetic ladders realized with one-dimensional alkaline-earth(-like) fermionic gases and subject to a gauge field represent a promising environment for the investigation of quantum Hall physics with ultracold atoms. We unveil the existence of a hierarchy of fractional insulating and conducting states by means of both analytical bosonization techniques and numerical methods based on the density-matrix renormalization group algorithm. We show that such states can be exploited for constructing a topological Thouless pump where the charge transported after one cycle is quantized to fractional values and demonstrate this behavior with a full many-body time-dependent calculation.

1 - S. Barbarino, L. Taddia, D. Rossini, L. Mazza, R. Fazio, Nat. Commun. 6, 8134 (2015)

2 - S. Barbarino, L. Taddia, D. Rossini, L. Mazza, R. Fazio, New J. Phys. 18, 035010 (2016)

3 - L. Taddia, E. Cornfeld, D. Rossini, L. Mazza, E. Sela, R. Fazio, in preparation

Ordered Phases in Coupled Driven Systems

Mustansir Barma (TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad, India)

Applications of Random Matrix Theory for high-dimensional statistics.

In the present era of Big Data, new statistical methods are needed to decipher large dimensional data sets that are now routinely generated in almost all fields – physics, image analysis, genomics, epidemiology, engineering and finance, to quote only a few. It is very natural to try to identify common causes that explain the joint dynamics of a large number of quantities. The primary aim of this thesis is to understand theoretically the so-called curse of dimensionality that describe phenomena which arise in high-dimensional space using Random Matrix Theory. Special care is devoted to the statistics of the eigenvectors of large noisy matrices, which turn out to be crucial for many applications. Moreover, I will present how to build reliable estimators that are consistent with the dimension of the problem. In the case of correlation matrices, the estimator we obtain provide better performance than all previously proposed methods for real-world applications within financial markets.

The spin one XXZ chain and symmetry classes of alternating sign matrices

Christian Hagendorf (Université Catholique de Louvain, Belgique)

Some new problems on random walks and exclusion processes

Ricardo Mendonça (Uni. de Sao Paolo)

In this informal talk I am going to present two problems related with random walks and exclusion processes: the longest-increasing subsequence (LIS) problem for random walks and the symmetric simple exclusion process in discrete time over graphs. The first problem corresponds to a new incarnation of the LIS problem for discrete i.i.d. variables (random permutations), but now with correlated variables, while the second problem touches on many interesting (and hard) problems in combinatorics, computer science, and graph theory. So far I have more questions than answers, so your attendance, comments and contributions are welcome!

Fluctuations in the flow of disordered solids and complex fluids: the ups and downs of simple models

Alexandre Nicolas (LPTMS)

Disordered solids, such as foams, concentrated emulsions and metallic glasses, are examples of complex systems made of complex entities. However, when describing or modelling their macroscopic response, most of the complexity of the entities under study can often be left aside. This applies in particular to the fluctuations in their flow. In this talk, I will present some successes and caveats associated with simple descriptions of these fluctuations.

A very broad class of materials, disordered solids span all damping regimes, from overdamped to underdamped. This fact calls for a clarification of the effect of inertia on their flow. The first part of my talk will be dedicated to showing that, macroscopically, the effect of inertia is identical to that of simple (but shear-rate-dependent) thermal fluctuatiions.

But this does not imply that any fluctuations can be modelled as thermal fluctuations. Accordingly, I will then insist on a caveat associated with these simple models, by questioning the popular description of the mechanical noise (i.e., the stress fluctuations induced local microruptures in the deformed material) as an effective activation temperature.

Finally, if time allows, I will very briefly touch upon fluctuations in a very different type of complex systems, namely, crowds of pedestrians, and the statistical fluctuations in evacuation times.

Active transport in complex environments

Pierre Illien (R. Peierls Centre for Theor. Phys., Oxford University, UK)

Network Reconstruction: the Contribution of Challenges in Machine Learning

Isabelle Guyon (Laboratoire de Recherche en Informatique, Université Paris-Sud)

Long-range correlations and anomalous heat transport in momentum conserving models

David Mukamel (Weizmann Institute of Science, Israël)

• Anupam Kundu, Ori Hirschberg and & Mukamel Long-range correlations in stochastic transport with energy and momentum conservation, J.Stat.Mech.: Theor. Exp., 033108 (2016)
• Julien Cividini, Anupam Kundu, A. Miron & David Mukamel, Temperature profile and boundary conditions in an anomalous heat transport model,  preprint cond-mat arXiv:1609.06614.

CTCF mediates allele-specific 3D domain structure at paternally imprinted gene loci

Daan Noordermeer (I2BC, Gif-sur-Yvette, France)

NOTE THE NEW LOCATION (due to renovation work at LPS)

Imprinted genes are mammalian genes where only one copy (allele) is active, depending on whether it is inherited from the mother or the father. This selective activity is determined by allele-specific DNA methylation at defined sites in the genome, so-called Imprinting Control Regions (ICRs). Recent microscopy studies by the group of Robert Feil (IGM-Montpellier, France) have revealed that imprinted genes are differently organized in the cell nucleus, depending on their parental origin (Kota et al., 2014). We have used high-resolution 4C-seq studies (Circular Chromosome Conformation Capture) to dissect the mechanisms and dynamics of this differential organization at the Dlk1-Dio3 and Igf2-H19 loci.

Recent studies have revealed that mammalian genomes are organized into Topologically Associating Domains (TADs) that demarcate ‘gene regulatory neighborhoods’ (Dixon et al., 2012). These physical domains are formed through a mechanism of ‘loop extrusion’ of the DNA fiber, with borders that are demarcated by opposing binding sites of the architectural CTCF protein (Fudenberg et al., 2016). I will show that the imprinted Dlk1-Dio3 and Igf2-H19 loci are organized into different DNA domains, determined by allele specific CTCF binding.

Both the Dlk1-Dio3 and Igf2-H19 loci are contained within large, invariant Topologically Associating Domains (TADs). The presence of the CTCF protein at the unmethylated ICRs on the maternal allele allows the establishment of new loops within the TADs. This result in the formation of a domain that acts like a cage, thereby shielding regulatory elements from nearby genes.

At the paternal alleles, DNA methylation at the ICR inhibits CTCF binding. As a result, the paternal Igf2-H19 allele displays little specific organization within the TAD. In contrast, at the paternal Dlk1-Dio3 locus, loops are formed between more distant unmethylated CTCF sites. The paternal allele therefore forms a much larger subdomain that is contained within the TAD.

Our work, for the first time, shows that constitutive TADs can have a markedly different allele-specific internal domain organization. Moreover, it shows that methylation-dependent DNA binding of the CTCF protein at ICRs guides the process of loop extrusion, thereby change the 3D structure of chromatin domains. We speculate that the imprinted patterns of gene expression at these loci are mostly imposed by the maternal 3D architecture, supporting previous genetic studies.

Statistical physics of molecular evolution: from gene regulation to immune system

Armita Nourmohammad (Lewis Sigler Institute, Princeton University)

Quantum motion of an impurity through a medium at zero temperature in one spatial dimension

Mikhail Zvonarev (LPTMS, Université Paris-Sud)

Modeling of phase transitions and patterns formation in ensembles of solitons

Peter Karpov (National University of Science and technology "MISiS", Moscow, Russia)

Optimal immune systems

Aleksandra Walczak (LPT-ENS, Paris)

NOTE THE NEW LOCATION (due to renovation work at LPS)

Biological organisms have evolved a wide range of complex strategies to defend themselves against pathogens. I will present a common evolutionary framework that balances the benefits and costs involved in protection against pathogenic environments to maximize the long growth rate of populations. I will show that such a general evolutionary perspective recovers the basic forms of known immunity. I will then focus on adaptive immunity which is based on a combinatorically encoded repertoire of receptors that protects organisms from a diverse set of pathogens. A well-adapted repertoire should be tuned to the pathogenic environment to reduce the cost of infections. I will discuss a general approach for predicting the optimal repertoire that minimizes the cost of infections contracted from a given distribution of pathogens.

Momentum space topology, anomalous quantum Hall effect, and the absence of equilibrium static chiral magnetic effect

Mikhail A. Zubkov (ITEP, Moscow, Russia & LMPT, Université François Rabelais, Tours)

• “Absence of equilibrium chiral magnetic effect”, Phys. Rev. D 93 (2016) no.10, 105036, doi:10.1103/PhysRevD.93.105036, arXiv:1605.08724 [hep-ph], by M. A. Zubkov
• “Wigner transformation, momentum space topology, and anomalous transport”, Annals Phys. 373 (2016) 298-324, doi:10.1016/j.aop.2016.07.011,  arXiv:1603.03665 [cond-mat.mes-hall],  by M. A. Zubkov

Ultimate limits of quantum measurements

Daniel Braun (Institut für Theoretische Physik, Universität Tübingen)

Dynamical non-Hermitian random matrices - Hydrodynamics and relevance of eigenvectors

Jacek Grela (LPTMS, Université Paris-Sud)

• "Dysonian dynamics of the Ginibre ensemble", Z. Burda, J. Grela, M. A. Nowak, W. Tarnowski, P. Warchol, Phys. Rev. Lett. 113, 104102 (2014)
• "Unveiling the significance of eigenvectors in diffusing non-hermitian matrices by identifying the underlying Burgers dynamics", Z. Burda, J. Grela, M. A. Nowak, W. Tarnowski, P. Warchol, Nucl. Phys. B 897, 421 (2015)
• "Hydrodynamical spectral evolution for random matrices", P.J. Forrester, J. Grela, J. Phys. A: Math. Theor. 49 085203 (2016)

How far from equilibrium is active matter?

Frédéric van Wijland (Laboratoire Matière et Systèmes Complexes, Université Paris 7 Denis Diderot)

The diversity of evolutionary rates

Jakub Otwinowski (Department of Biology, University of Pennsylvania, Philadelphia)

Collective oscillations of trapped atomic gases in low dimensions: a tool for the investigation of collisional processes

Giulia De Rosi (Università di Trento, Italia)

• G. De Rosi and S. Stringari, Collective oscillations of a trapped quantum gas in low dimensions, Phys. Rev. A 92 , 053617 (2015).
• G. De Rosi and S. Stringari, Hydrodynamic VS collisionless dynamics of a 1D harmonically trapped Bose gas, to appear in Phys. Rev. A, preprint arXiv:1608.08417

Deficient ribosome biogenesis is an early marker of cellular senescence

Sandrine Morlot (IGBMC, Strasbourg)

NOTE THE NEW LOCATION (due to renovation work at LPS)

Saccharomyces cerevisiae is a powerful model organism to study replicative aging as asymmetric division gives rise to an aging mother cell and a rejuvenated daughter cell [Mortimer and Johnston 1959, Egilmez and Jazwinski 1989]. However the cellular mechanisms controlling replicative lifespan and the rejuvenation process are still poorly understood partly due to the technical limitations of following individual cells from birth to death. In this context, we have developed a high-throughput microfluidic device to follow up to 3200 single cells in parallel throughout their lifespan under the microscope. Thanks to this technology, we have established a timeline of events occurring successively during cellular aging. We have observed that cells experience a sharp transition into senescence. Indeed yeasts divide regularly every 90 minutes until a senescence entry point (SEP) which occurs after 20 generations. After this point, cell cycles strongly slow down until death [Fehrmann et al. Cell Reports 2013]. Furthermore we have measured that the SEP is preceded by an abrupt increase in the nuclear volume and more specifically in the size of nucleolus. The nucleolus is the nuclear compartment where ribosome biogenesis is initiated. This age-dependent nuclear defect is retained by the mother only, as daughter cells recover a normal nucleus and nucleolus, in agreement with the daughter cell rejuvenation paradigm. We have characterized that pre-ribosome particles accumulate in the nucleolus approximately 10 hours before entering into senescence. Our analysis suggests that this deficiency in ribosome biogenesis triggers cellular senescence.

Emergent anyons in quantum Hall physics

Nicolas Rougerie (LPMMC, Université de Grenoble)

• Douglas Lundholm and Nicolas Rougerie, "Emergence of Fractional Statistics for Tracer Particles in a Laughlin Liquid", Phys. Rev. Lett. 116, 170401 (2016)

The Physics of Active Matter

Julien Tailleur (Laboratoire Matière et Systèmes Complexes, Université Denis-Diderot)

High-fidelity computational modelling of biofilms and fibre networks

David Head (University of Leeds, UK)

NOTE THE NEW LOCATION (due to renovation work at LPS)

Mathematical models of complex systems can help develop fundamental insight and accelerate the development of novel materials and therapeutic treatments, but the simplifications that must necessarily be made reduce both validity and predictability, even for complex models that are solved numerically. Here I will describe recent results in two research streams aimed at developing and validating high-fidelity in silico models for biofilms and fibre networks, aiming to reduce the realism gap to experimental systems while maintaining sufficient performance to permit solution for times and system sizes of interest. The first is a bespoke model for biofilms in which mechanical relaxation between cells replaces the "pushing" rules typically used, and has been applied to the archetypal biofilm of dental plaque, revealing insight into long-term ecological dynamics not easily assayed experimentally. Secondly, I will discuss dynamic simulations of peptide gels and collagen hydrogel scaffolds, both having important applications as novel biomaterials but where network formation must also be simulated to better approximate the experiments; reaching realistic time scales is a substantial challenge.

Topological insulators and semimetals

Andrei Bernevig (Princeton University, USA)

Nonlinear polarization waves in two-component Bose-Einstein condensates

Thibault Congy (LPTMS, Université Paris-Sud)

Truncated linear statistics associated with the top eigenvalues of random matrices

Aurélien Grabsch (LPTMS, Université Paris-Sud)

Mechanosensing: insights from experimental physics at the single-cell scale

Atef Asnacios (MSC, Université Paris-Diderot, France)

NOTE THE NEW LOCATION (due to renovation work at LPS)

As part of their physiological functions, most cells need to adapt to their mechanical environment. In particular, the rigidity of the extracellular matrix was shown to control cell traction forces, shape, and ultimately cell differentiation. In this context, most studies focused on the role of biochemical regulation in rigidity sensing.

In contrast to this biochemical signaling-centered approach, our aim is to reveal the physical/mechanical phenomena involved in mechanosensing. To this end, we have developed original single-cell techniques combining mechanical measurements (traction force, mechanical power…) with monitoring of cell structures (evanescent wave microscopy). In particular, we have designed a unique protocol allowing us to change the effective stiffness felt by a single cell in real time (~0.1 second), thus allowing us to show that an early purely mechanical response of single cell to stiffness indeed does exist.

We will present the results of experiments combining single-cell traction force measurements, dynamic control of stiffness, and monitoring of adhesion complexes, and will discuss how cell shape (~ contact angle) and mechanical adaptation to rigidity (~ impedance matching) could control cell fate.

Phases and phase transitions on disordered Bethe lattice: analytical treatment by one-step replica symmetry breaking

Vladimir Kravtsov (ICTP, Trieste, Italy)

• B. L. Altshuler, L. B. Ioffe and V. E. Kravtsov, Multifractal states in self-consistent theory of localization: analytical solution, preprint arXiv:1610.00758

Optimal structure and parameter learning of Ising models and calibration of the D-Wave quantum computer

Andrey Lokhov, Los Alamos National Laboratory

Reconstruction of structure and parameters of a graphical model from binary samples is a problem of practical importance in a variety of disciplines, ranging from statistical physics and computational biology to image processing and machine learning . The focus of the research community shifted towards developing universal reconstruction algorithms which are both computationally efficient and require the minimal amount of expensive data. In this talk, we introduce a new method, Interaction Screening, which accurately estimates the model parameters using local optimization problems. We provide mathematical guarantees that the algorithm achieves perfect graph structure recovery with an information-theoretically optimal number of samples and outperforms state of the art techniques, especially in the low-temperature regime which is known to be the hardest for learning. As an application, we show how the method can be used for an efficient calibration of the D-Wave quantum computer.