Stochastic lattice gases (interacting particle systems) are used to model transport phenomena, where one starts from defining microscopic rules and tries to show behaviors of macroscopic quantities. The macroscopic evolution of a stochastic lattice gas with symmetric hopping rules is described by a diffusion equation with density-dependent diffusion coefficient. In practice, even when the equilibrium properties of a lattice gas are analytically known, the diffusion coefficient cannot be explicitly computed, except for a few simple examples, e.g. for the symmetric simple exclusion process. We develop a procedure to systematically obtain approximations for the diffusion coefficient in explicit forms. The method relies on a variational formula found in mathematics literature. Restriction on test functions to finite-dimensional sub-spaces allows one to perform the minimization and gives upper bounds for the diffusion coefficient. We demonstrate calculations in the following two models; one-dimensional generalized exclusion processes, where each site can accommodate at most two particles (2-GEPs) [1], and the Kob-Andersen (KA) model on the square lattice, which is classified into kinetically-constrained gas [2]. The prediction of the diffusion coefficient depends on the domain ("shape") of test functions. The smallest shapes give approximations which coincide with the mean-field theory, but the larger shapes, the more precise upper bounds we obtain. For the 2-GEPs, our analytical predictions provide upper bounds which are very close to simulation results throughout the entire density range. For the KA model, we also find improved upper bounds when the density is small. By combining the variational method with a perturbation approach, we discuss the asymptotic behavior of the diffusion coefficient in the high density limit.

[1] CA, P L Krapivsky, K Mallick: Phys. Rev. E 95, 032121 (2017)
[2] CA, P L Krapivsky, K Mallick: J. Phys. A (accepted)

Pb1-xSnxSe (x>0.16) topological crystalline insulators host massless surface Dirac cones stemming from a band inversion that occurs at the mirror symmetric L-points of the Brillouin zone [1], [2]. In this talk, I will present two experimental observables related to the emergence of the topological phase in Pb1-xSnxSe. First, I will show how bulk transport is uniquely altered by the band inversion, and exhibits a negative magnetoresistance when the system is in the quantum limit [3]. Second, I will demonstrate the emergence of topological interface states at a topological-trivial junction formed between Pb0.75Sn0.25Se and Pb1-yEuySe. Using infrared Landau level spectroscopy, I will present our results evidencing the robustly Dirac-like nature of these surface states up to 15T, and their mass acquisition and suppression as a function of increasing temperature and quantum confinement [4]. Overall, I will argue throughout my talk that Pb1-xSnxSe is – truly – a model system to study topological phase of matter.
[1] T. Hsieh et al. Nature Comm. 3 982 (2012)
[2] B.A. Assaf, T. Phuphachong et al. npj Quantum Materials 2 26 (2017)
[3] B.A. Assaf, T. Phuphachong et al. Phys. Rev. Lett. 119 106602 (2017)
[4] G. Krizman, B.A. Assaf et al. in preparation

The DNA shows a high degree of spatial and dynamical organization over a broad range of length scales. It interacts with different populations of proteins and can form protein-DNA complexes that underlie various biological processes, including chromosome segregation. A prominent example is the large ParB-DNA complex, an essential component of a widely spread mechanism for DNA segregation in bacteria. Recent studies suggest that DNA-bound ParB proteins interact with each other and condense into large clusters with multiple extruding DNA-loops.

In my talk, I present the Looping and Clustering model, a simple statistical physics approach to describe how proteins assemble into a protein-DNA cluster with multiple loops. Our analytic model predicts binding profiles of ParB proteins in good agreement with data from high precision ChIP-sequencing – a biochemical technique to analyze the interaction between DNA and proteins at the level of the genome. The Looping and Clustering framework provides a quantitative tool that could be exploited to interpret further experimental results of ParB-like protein complexes and gain some new insights into the organization of DNA.

High-energy processes at the LHC are potentially powerful indirect probes of heavy new physics, whose effects can be encapsulated in higher-dimensional operators or in modified Standard Model couplings. The energy growth of new-physics effects in a broad class of processes makes them sensitive targets of the LHC large kinematic reach, provided accurate enough measurements are possible. In this talk I give an overview of this topic and discuss, in particular, how dilepton and diboson processes can allow us to obtain precision electroweak measurement at the LHC and future colliders.

Since the last decades, scientists can manipulate single polymer molecules. This amazing possibility allows the direct measure of very small forces and displacements, opening the way for studying the statistical mechanics of small systems. In many cases in which the thermodynamic limit is not satisfied, different macroscopic boundary conditions (i.e. constant-force or constant-displacement) may yield to different force-displacement curves. This point has a crucial impact on many experimental results [1].
Such an impact is shown to be extremely suggestive when dealing with bistable molecules, composed of a series combination of domains that can exhibit transitions between two stable states.
This scenario leads from a cooperative to non-cooperative force-extension behavior of the molecule, depending on its size and the specific boundary conditions [2]. In particular, I will show that for short molecules, the domain response is non-cooperative and originates the typical “sawtooth” force-extension curve, as observed for the titin protein. On the other hand, upon increasing molecule length, the response of each domain is cooperative and results in a “plateaulike” curve, as observed for the dextran polysaccharide. Our theoretical framework provides a unified picture for such apparently contrasting experimental situations.
Finally, I will discuss the cooperative behavior of a system composed of a parallel combination of bistable domains that share two rigid points. As an important biophysical application, I will focus on the role of SNARE proteins in neurotransmission. These proteins can perform synchronized and explosive conformational changes, triggering the neurotransmission process in a millisecond timescale.
By means of a kinetic model that retains the biophysical key properties of the SNAREs bistability, we studied their stochastic dynamics and predicted the existence of a minimum timefusion as a function of the number of SNAREs involved. We found that N = 5 ± 1 is the optimal number of SNAREs required to catalyze fusion within 0.1 milliseconds [3]. This optimum is due to the intrinsic bistabilty of SNAREs and can be one of the major physiological principle governing the quick timescale of neurotransmitter release.


[1] F. Manca, S. Giordano, P. L. Palla, R. Zucca, F. Cleri, L. Colombo, Elasticity of flexible and
semi-flexible polymers with extensible bonds in the Gibbs and Helmholtz ensembles, J. Chem. Phys.
136, 154906 (2012).
[2] F. Manca, S. Giordano, P. L. Palla, F. Cleri, L. Colombo, Two-state theory of single-molecule
stretching experiments, Phys. Rev. E 87, 032705 (2013).
[3] F. Manca, F. Pincet, L. Truskinovsky, J.E. Rothman, L. Foret, M. Caruel, Optimal number of
SNARE proteins for fast neurotransmetter release, to be submitted in PNAS

The inner cavity of nanotubes attracted a lot of interest as template for the encapsulation of elongated dyes molecules, such as polythiophenes. Indeed, the 1D confinement drives the stacking of the molecules inside and enables original aggregation effects on their optical properties (1,2). When encapsulated inside carbon nanotube, organics dyes such as 6T exhibits for example a strong and specific Raman scattering but their luminescence is efficiently quenched by the nanotube (3). Here we show that the same dyes, when encapsulated inside boron nitride nanotubes (6T@BNNT) exhibits strong luminescence (4). Photoluminescence imaging experiments on individualized 6T@BNNT deposited on substrate show that the encapsulation also circumvent the photobleaching issue over days under continuous photo-excitation. Finaly we show that these hybrid materials can act as robust nanoprobes with reduced toxicity in living system such as Daphnia Pulex, for multimodal imaging. (4)

(1) E. Gaufrès et al Nature Photon. (2014)
(2) S. Cambré et al Nature Nano (2015)
(3) E. Gaufrès et al ACS Nano (2016)
(4) E. Gaufrès et al (submitted)

Dans ce séminaire, je présenterai de nouvelles relations universelles pour la production d'entropie de systèmes mésoscopiques qui sont entraînés arbitrairement loin de l'équilibre thermique. Ceux-ci comprennent les théorèmes de fluctuation temporelle de premier passage et les lois d'infimum pour la production d'entropie. Nous discuterons des applications à la dynamique des particules colloïdales, des moteurs moléculaires et des dispositifs microélectroniques. Dans une seconde partie, je présenterai comment les théorèmes de fluctuation temporelle de premier passage peuvent être utilisés pour tester l'optimalité des systèmes prenant des décisions séquentielles. Dans une dernière partie, je présenterai une étude de la signalisation dans le système endosomal.

Since the first experimental evidence of photoluminescence of semiconducting single-walled carbon nanotubes (SWNTs), studies have been conducted to investigate the optical properties of these nano-structures, motivated by possible applications in the fields of quantum information, biological labeling, opto-electronics or laser technology. The experimental investigation of the intrinsic optical properties of SWNTs is challenging since they are extremely sensitive to the influence of their physico-chemical environment. In this context, samples with reduced perturbations, such as suspended SWNTs, are particularly interesting.
In this talk, I will present an experimental study of the magneto-optical properties of suspended SWNTs through time-resolved photoluminescence spectroscopy. Measurements are performed at the single-object level using a home-built confocal optical microscope with a large numerical aperture (NA = 0.95) operating at cryogenic temperature (down to 2K) and high magnetic field (up to 7T). The evolution of the photoluminescence spectra and decay signals with increasing magnetic fields shows the influence of the Aharonov-Bohm effect on the two lowest-energy singlet excitons, namely the ground exciton which is optically inactive (dark exciton) and an exciton lying a few millielectronvolts higher in energy which is optically active (bright exciton). A model based on rate equations and including the Aharonov-Bohm coupling between these two excitons enables to determine separately the excitons lifetimes and to derive quantitative information on the energy relaxation from the photo-excited higher levels. The energy relaxation following the photo-excitation of the S22 transition leads to a bright state population efficiency four times lower than that of the dark state, but it significantly increases when energy relaxation occurs from the KK’ excitonic levels. Thanks to a good signal to noise ratio, the photoluminescence spectra also reveal the presence of a very weak intrinsic zero-field coupling between the dark and the bright excitons, as well as an excitonic mobility preserved at liquid helium temperature in suspended SWNTs.

The mechanical properties of epithelial tissues, which are typically composed of a single layer of tightly bound cells, play an important role in development and disease. Therefore, our goal is to develop theoretical and computational tools to help explain global mechanical behavior and cell migration patterns in these tissues. In this talk, I will focus on connections between tissue rigidity and collective migration using two different techniques in two different geometries. In the first project, we develop a hydrodynamic model for bulk tissues that couples cell shapes, tissue rigidity, and cell-substrate interactions by assuming that cells exert traction forces preferentially along gradients in the in-plane tissue stiffness, in accord with recent experiments. Analyzing the steady states of the model, we identify a new “morphotactic” parameter that our model predicts will control pattern formation in real tissues. In the second project, we developed a new active vertex model and employed it to simulate so called “wound-healing” experiments in which a tissue is allowed to expand into free space. These simulations indicate that tissues are unable to sustain a mechanical stress in the absence of propulsive forces generated by cell-substrate interaction. Further, our results suggest that polar order in these propulsive forces qualitatively changes the observed stress profile, and may thereby promote cell proliferation.